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Cedex Analyzer

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Cedex Analyzer Addendum 2 to Operator’s Guide Version 1.0 Software Version 2.2.1 For life science research only. Not for use in diagnostic procedures. August 2012 Information regarding the Cedex Analyzer Dear Valued User of the Cedex Analyzer, Roche Diagnostics Ltd. has merged into Roche Diagnostics International Ltd and therefore the company name has changed to Roche Diagnostics International Ltd In order to harmonize and improve our support, the legal manufacturer changes as follows: Roche Diagnostics GmbH Sandhofer Strasse 116 68305 Mannheim Germany If you have any further questions regarding this matter, please do not hesitate to contact your Roche Diagnostics representative. To call, write, fax, or email us, visit the Roche Applied Science home page, http://www.roche-applied-science.com and select your home country. Country-specific contact information will be displayed. The address of the legal manufacturer in section “Prologue/Contact Addresses” changes as follows: New adress Roche Diagnostics Ltd. Forrenstrasse CH-6343 Rotkreuz Switzerland Roche Diagnostics GmbH Sandhofer Strasse 116 68305 Mannheim Germany 06845967001 a 0812 Old adress CEDEX and INNOVATIS are trademarks of Roche. For life science research only. Not for use in diagnostic procedures. ©2012 Roche Diagnostics. All rights reserved. Cedex Analyzer Addendum 1 to Operator’s Guide, Version 1.0 Software Version 2.2.1 For life science research only. Not for use in diagnostic procedures. January 2012 Information Regarding the Cedex Analyzer Operator’s Guide Please read the following information, which updates information given in the Cedex Analyzer Operator’s Guide Dear valued user of the Cedex Analyzer This addendum includes: c Updated information about the procedure for removal, reinstallation or replacement of the syringe. If you have any further questions regarding this matter, please do not hesitate to contact our Technical Services Department at your best convenience. To call, write, fax, or email us, visit the Roche Applied Science home page, http://www.roche-applied-science.com and select your home country. Country-specific contact information will be displayed. Syringe Maintenance Section E: Maintenance and Care Chapter 5: Syringe Maintenance Follow the syringe maintenance procedure described on pages 128 – 129 to remove, reinstall or replace the syringe of the Cedex System. After removal, reinstallation or replacement of the syringe, a calibration check of the Cedex System must also be performed. Use Cedex Density Reference Standard Beads to check the calibration and confirm that the FlowFactor is correct. If necessary, adjust the FlowFactor. To perform the Cedex System calibration check and FlowFactor adjustment, follow the instructions described in the online Instructions for Use for the Density Reference Standard Beads, available for download at: https://www.roche-applied-science.com/PROD_INF/index.jsp?&id=iforu Ordering Information Product Pack Size Cat. No. Density Reference Standard Beads 1× 10 ml Batch A 06 422 659 001 Density Reference Standard Beads 1× 10 ml Batch B 06 422 667 001 E Maintenance and Care 3 For life science research only. Not for use in diagnostic procedures. CEDEX and INNOVATIS are trademarks of Roche. Published by Roche Diagnostics GmbH Sandhofer Straße 116 68305 Mannheim Germany © 2012 Roche Diagnostics. All rights reserved. www.roche-applied-science.com 06638589001  0112 Cedex Analyzer Operator’s Guide Software Version 2.2.1 For life science research only. Not for use in diagnostic procedures. May 2011 Table of Contents Prologue 9 I. Revision History ................................................................................................................................................................ 9 II. Contact Addresses .......................................................................................................................................................... 9 III. Declaration of Conformity .........................................................................................................................................10 IV. Warranty ..............................................................................................................................................................................11 V. Trademarks ........................................................................................................................................................................11 VI. Copyrights ..........................................................................................................................................................................11 VII. Intended Use .....................................................................................................................................................................11 VIII. Software License Agreement ..................................................................................................................................12 IX. Preamble .............................................................................................................................................................................15 X. Contents of this Operator’s Guide ........................................................................................................................15 XI. Conventions used in this Guide .............................................................................................................................15 XII. FCC Notification ..............................................................................................................................................................16 XIII. Warnings and Precautions ........................................................................................................................................ 17 XIV. Disposal of the Analyzer ............................................................................................................................................18 A Overview 1 Description of the Cedex System ..........................................................................................................................20 2 The Measurement Procedure ..................................................................................................................................21 2.1 19 The Trypan Blue Exclusion Method .............................................................................................................................21 3 Data Analysis ..................................................................................................................................................................22 4 Technical Specifications of the Analyzer ..........................................................................................................23 B System Description 1 Installing the Cedex System ....................................................................................................................................25 2 25 Choosing a Suitable Location .................................................................................................................................26 2.1 3 Connecting or disconnecting the device ..................................................................................................................26 Connecting Hardware Components .................................................................................................................... 27 3.1 Completing the Windows Mini-setup ........................................................................................................................28 4.1 4.1.1. 4.2 4.3 4.3.1. 4.3.2. 4.3.3. Installing the Cedex Software 2.2 ................................................................................................................................29 Setting the Cedex Server to Autostart .......................................................................................................................33 Starting up the Software .................................................................................................................................................34 Updating Older Cedex Software version 2.x to Cedex Software 2.2 ...............................................................35 Overview ...............................................................................................................................................................................35 Updating to Cedex Software 2.2...................................................................................................................................35 Restoring a Cedex Software 2 Backup ......................................................................................................................39 4 Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 ....................................................29 5 Starting the Cedex System after installation ..................................................................................................41 6 Securing Access Rights ............................................................................................................................................42 6.1 6.2 Access Control at the Windows Operating System Level ...................................................................................42 Access Control at the Cedex System Software Level ...........................................................................................42 3 Table of Contents C Operation 1 Overview of the Cedex Control Center...............................................................................................................43 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 2 Menu Bar ..............................................................................................................................................................................43 System Menu .......................................................................................................................................................................43 Measurement Menu .........................................................................................................................................................44 Functions Menu..................................................................................................................................................................44 Reports Menu ....................................................................................................................................................................45 Master Data Menu ............................................................................................................................................................45 Setup Menu .........................................................................................................................................................................45 Help Menu ............................................................................................................................................................................46 Shortcuts Area ....................................................................................................................................................................46 Tracking of Status of Events Carried out by the Analyzer ..................................................................................46 Preparing the Analyzer for Measurements ...................................................................................................... 47 2.1 2.2 2.3 2.4 2.5 2.5.1. 2.5.2. 2.6 3 Switching on ........................................................................................................................................................................ 47 Logging in at the Computer Operating System Level .......................................................................................... 47 Starting the Cedex Software 2.2 ................................................................................................................................. 47 Performing a HW Startup and Prime..........................................................................................................................48 Preparing the Reagent Kit ..............................................................................................................................................49 Installing or Changing the Reagent Kit ....................................................................................................................49 Refilling Containers Individually ..................................................................................................................................51 Checking the Analyzer .....................................................................................................................................................52 Carrying out a Single Measurement ...................................................................................................................53 3.1 3.2 3.3 3.3.1. 3.3.2. 3.4 4 Opening the Measurement window and specifying the Operating Mode and Sample Data ..............54 Defining the Measurement and Analysis (Process) Parameters .....................................................................55 Preparing the Sample and Attaching it to the Multi Sample Tray or Sample Port ....................................56 Starting the Measurement .............................................................................................................................................56 End of Measurement ........................................................................................................................................................ 57 Interrupting a Measurement..........................................................................................................................................58 Working with the Multi Sampler ............................................................................................................................59 4.1 4.2 4.2.1. 4.2.2. 4.2.3. 4.3 4.3.1. 4.3.2. 4.3.3. 4.3.4. 4.3.5. 4.3.6. 4.4 4.5 4.6 4.6.1. 5 The Multi Sampler DefaultCup .....................................................................................................................................60 Preparing the Measurement ..........................................................................................................................................61 Using the Multi Sample Tray..........................................................................................................................................61 Ejecting the Multi Sample Tray .....................................................................................................................................61 Performing a Prime ..........................................................................................................................................................61 Carrying out Measurements with the Multi Sampler ...........................................................................................61 The Multi Run Data Entry Window ..............................................................................................................................61 Preparing for Multiple Measurements in the Multi Run Window ...................................................................62 Activating Sample Rows and Starting the Measurement...................................................................................63 Adding Measurements to the List while Measurements are Running .........................................................64 Modifying Data Entry, Changing Samples ..............................................................................................................65 Non-Linear Measurements in a Sample Series ....................................................................................................65 Interrupting a Multi Run..................................................................................................................................................65 Disruption of Measurements.........................................................................................................................................65 Results ...................................................................................................................................................................................66 The Multi Run Result List................................................................................................................................................66 Switching off the Cedex Analyzer ........................................................................................................................ 67 5.1 5.2 5.3 4 43 Carrying out an LM Shutdown and HW Shutdown .............................................................................................. 67 Logging out ..........................................................................................................................................................................68 Shutting down the Control Center ..............................................................................................................................68 Cedex Analyzer Operator’s Guide Table of Contents D Software 1 Using the Measurement Results Window ........................................................................................................69 1.1 1.2 1.3 1.3.1. 1.3.2. 1.3.3. 2 69 Result Data area................................................................................................................................................................. 70 Sample Parameters and Processing Parameters areas .......................................................................................71 Image Area ...........................................................................................................................................................................72 Viewing Individual Cell Images .....................................................................................................................................72 Viewing a Cell Image Using the Image View Window ........................................................................................73 Excluding Images from the Evaluation Process/Including Excluded Images ............................................. 74 Using the Measurement List....................................................................................................................................75 2.1 2.2 3 Viewing Existing Analysis Results ............................................................................................................................... 76 Searching for Measurements ........................................................................................................................................ 76 Editing Existing Analysis Results/Data Sets ................................................................................................... 77 3.1 3.2 4 The Reprocess Button ...................................................................................................................................................... 77 Effective Data Sets ............................................................................................................................................................ 78 Graphical Display of the Analysis Results........................................................................................................ 79 4.1 4.2 4.3 4.3.1. 4.4 4.5 4.6 5 Enlarging the Histograms ............................................................................................................................................... 79 Aggregate Histogram .......................................................................................................................................................80 Cell Diameter Histogram .................................................................................................................................................82 Defining Diameter Intervals in the Diameter Histogram.....................................................................................83 Object Diameter Histogram ...........................................................................................................................................83 Compactness Histogram .................................................................................................................................................84 Measurement Statistics Histogram .............................................................................................................................85 Cultivation Time Chart .................................................................................................................................................86 5.1 5.1.1. 5.1.2. 5.1.3. 5.1.4. 5.1.5. 5.1.6. 5.1.7. 5.2 5.2.1. 5.2.2. 5.2.3. 5.2.4. 5.2.5. 5.2.6. 6 Creating a CTC View .........................................................................................................................................................86 The View Area ..................................................................................................................................................................... 87 The Series of Measurements Belonging to Selected View Area ..................................................................... 87 Adding Measurements to a View ................................................................................................................................88 Editing Measurements in a View .................................................................................................................................89 Viewing List of Measurements in a Series ...............................................................................................................89 Deleting Views and Series ..............................................................................................................................................90 Exporting a View ................................................................................................................................................................90 Creating a Cultivation Time Chart ...............................................................................................................................90 The Data Selection Area .................................................................................................................................................91 Fitting to the Lowest Common Value .........................................................................................................................92 Measurement Series Offset ...........................................................................................................................................92 Variable Axis Calibration .................................................................................................................................................93 The Exponential Regression Button ............................................................................................................................93 Printing out a Cultivation Time Chart .........................................................................................................................93 General Functions of the System ..........................................................................................................................94 6.1 6.1.1. 6.1.2. 6.2 6.2.1. 6.2.2. 6.3 6.4 6.4.1. 6.4.2. 6.4.3. 6.4.4. 6.5 Data Management ............................................................................................................................................................94 Printing Reports..................................................................................................................................................................94 Export to file .........................................................................................................................................................................95 Data Exchange ....................................................................................................................................................................95 Export ....................................................................................................................................................................................96 Import ..................................................................................................................................................................................... 97 Viewing and Evaluating the Audit Trail File .............................................................................................................. 97 User Preferences ................................................................................................................................................................98 Adjusting Result Display in the Measurement List and Multi Run windows..............................................98 Specifying Default Measurement Parameters ........................................................................................................99 Specifying Other Default Parameters .........................................................................................................................99 Specifying the Workarea for the Analysis Data ....................................................................................................100 Changing own Password ..............................................................................................................................................100 5 Table of Contents D Software 7 Administrator Functions .......................................................................................................................................... 101 7.1 7.1.1. 7.1.2. 7.1.3. 7.1.4. 7.1.5. 7.2 7.2.1. 7.2.2. 7.3 7.4 7.4.1. 7.4.2. 7.4.3. 7.4.4. 7.4.5. 7.4.6. 7.4.7. 7.5 7.5.1. 7.5.2. 7.5.3. 7.5.4. 7.5.5. 7.5.6. 7.5.7. 7.5.8. 7.6 7.6.1. 7.6.2. 7.6.3. 6 continued Administration of User Accounts.............................................................................................................................. 101 Creating User Accounts .............................................................................................................................................. 101 Assigning Access Rights ..............................................................................................................................................102 Creating user groups ......................................................................................................................................................103 Editing and Deleting User Accounts ........................................................................................................................103 Creating and Editing User roles ................................................................................................................................ 104 Password Management .................................................................................................................................................105 Specifying Password Characteristics ........................................................................................................................105 Assigning New Passwords ...........................................................................................................................................105 Assigning Work Areas................................................................................................................................................... 106 The System Options ........................................................................................................................................................107 Automatically Start the Hardware Management .................................................................................................107 Modifying the Standard Setting for the Multi Sampler DefaultCup .............................................................107 Turning off Automatic Incrementation of Sample Cup Position .................................................................... 108 Error Level Displayed to Users ................................................................................................................................... 108 Liquid Container Configuration ................................................................................................................................. 108 Disabling the Reagent Control .................................................................................................................................. 109 Default Settings ............................................................................................................................................................... 109 Adjustment of the Image Analysis using the Live Operator ........................................................................... 109 Description of the Cell Type List and Live Operator .......................................................................................... 109 The Cell Type List Window ............................................................................................................................................110 Creating a New Cell Type..............................................................................................................................................111 Editing an Existing Cell Type ........................................................................................................................................112 Viewing an Existing Cell Type ......................................................................................................................................112 Deleting an existing Cell Type .....................................................................................................................................113 Working with the Live Operator..................................................................................................................................113 Description of the Individual Operator Parameters ............................................................................................115 Archiving Data .................................................................................................................................................................117 Archive .................................................................................................................................................................................117 Restore .................................................................................................................................................................................118 Deleting Archived Data .................................................................................................................................................118 Cedex Analyzer Operator’s Guide Table of Contents E Maintenance and Care 1 Cleaning and Maintenance Check List............................................................................................................120 2 Scheduling Automatic Cleaning Routines .....................................................................................................121 3 Daily and Manual Maintenance and Cleaning Routines .......................................................................... 122 3.1 3.2 3.2.1. 3.2.2. 3.2.3. 3.2.4. 3.3 119 Checking the Reagent Containers when Manually Refilling ...............................................................................122 Cleaning Routines Carried out by the Liquid Management ............................................................................122 Cleaning Options .............................................................................................................................................................123 The Hardware Management Window ......................................................................................................................124 Carrying out a Cleaning Routine ................................................................................................................................124 Interrupting/Terminating a Cleaning Routine........................................................................................................125 Live View of the Flow Chamber ..................................................................................................................................125 4 Automatic Adjustment ..............................................................................................................................................126 5 Syringe Maintenance .................................................................................................................................................128 5.1 5.2 5.3 Removing the Syringe ....................................................................................................................................................128 Assembling and Installing the Syringe ....................................................................................................................129 Maintenance of the Syringe Guide and Spindle ................................................................................................. 130 6 Maintenance of the Flow chamber, Microscope Optic, 8-Way Valve and the remaining Hardware Components ....................................................................................................... 131 7 Operational Data ......................................................................................................................................................... 131 8 The System Suitability Test (SST) ......................................................................................................................132 8.1 8.1.1. 8.1.2. 8.1.3. 8.2 8.2.1. 8.2.2. 8.3 8.3.1. 8.3.2. 8.4 Creating SST Checkpoints............................................................................................................................................132 Creating SST Checkpoints With and Without Measurements ........................................................................133 Running a Water Blank ............................................................................................................................................... 134 Setting up the SSTFailureReaction in the System Options Menu ................................................................ 134 Performing an SST...........................................................................................................................................................135 Performing an SST with Measurements .................................................................................................................135 Performing an SST without Measurements .......................................................................................................... 136 Tracking Trends in SST Results over Time............................................................................................................. 136 Tracking Trends in SST Checkpoints with Measurements .............................................................................. 136 Tracking SST Checkpoints without Measurements ........................................................................................... 138 Locking – Unlocking the System............................................................................................................................... 139 F Troubleshooting 141 1 Diagnosis of the Cedex Analyzer ....................................................................................................................... 141 2 Trace and Logging........................................................................................................................................................142 3 The System Audit Trail File ......................................................................................................................................142 G Appendix 1 System Options und User Preferences ............................................................................................................143 143 Index ................................................................................................................................................................................... 154 7 8 Cedex Analyzer Operator’s Guide Revision History Prologue I. Revision History Version Revision Date 1.0 May 2011 © Copyright 2011, Roche Diagnostics GmbH. All rights reserved. Information in this document is subject to change without notice. No part of this document may be reproduced or transmitted in any form or by any means, electronic or mechanical, for any purpose, without the express written permission of Roche Diagnostics GmbH. Questions or comments regarding the contents of this Operator’s Guide can be directed to your local Roche Diagnostics representative. Every effort has been made to ensure that all the information contained in the Cedex System Operator’s Guide is correct at the time of printing. However, Roche Diagnostics GmbH reserves the right to make any changes necessary without notice as part of ongoing product development. II. Contact Addresses Manufacturer Roche Diagnostics Ltd. Forrenstrasse CH-6343 Rotkreuz Switzerland Distribution Roche Diagnostics GmbH Sandhofer Straße 116 D-68305 Mannheim Germany Distribution in USA Roche Diagnostics 9115 Hague Road PO Box 50457 Indianapolis, IN 46250 USA Prologue 9 Declaration of Conformity III. 10 Declaration of Conformity Cedex Analyzer Operator’s Guide Warranty IV. Warranty The warranty conditions are specified in the sales contract. Contact your Roche Diagnostics representative for further information. Any unauthorized modification of the Cedex Analyzer and/or the Cedex Software will result in invalidity of the guarantee and service contract. V. Trademarks CEDEX and INNOVATIS are trademarks of Roche. Other brands or product names are trademarks of their respective holders. VI. Copyrights Cedex Analyzer Operator’s Guide. Copyright© 2011 Roche Diagnostics GmbH. All rights reserved. Operating instructions and manuals are protected by copyright. No part of this document may be reproduced, edited or translated without prior written consent of Roche Diagnostics GmbH except as permitted under the terms of the copyright. VII. Intended Use The Cedex Analyzer automatically determines the cell concentration and viability of cell suspensions for the purpose of life science research only. The Cedex Analyzer is for life science research only. Not for use in diagnostic procedures. It was neither developed nor validated by the manufacturer for any kind of in vitro diagnostic application. Prologue 11 Software License Agreement VIII. Software License Agreement Read the following terms and conditions of this Software License Agreement (“Agreement”) carefully before installing the Cedex 2 Software, hereinafter referred to as (“Software”). Proceeding with the installation of the Software will constitute acceptance of the terms and conditions of this Agreement. By accepting the terms and conditions of this Agreement, the end user (“Licensee”) assumes all responsibility and liability for the selection of this Software to achieve the intended results, and for its installation and subsequent use. If Licensee is not willing to be bound by the terms and conditions of this Agreement, the Software package must be promptly returned to Roche (“Supplier”) with a copy of the receipt against refunding of the purchase price for this Software. 1. Programm License Agreement Licensee assumes all responsibility and liability for the selection of this Software to achieve the intended results, and for its installation and subsequent use. The Software is protected by copyright. 2. Grant of Software License Supplier is entitled to grant to Licensee subject to continuous compliance with all the provisions hereinafter, a non exclusive, single use license to use the Software upon the terms and conditions contained in this Agreement. Licensee may: a. Use the Software on workstations which have to be owned, leased or otherwise controlled by Licensee, whether in a network or other configuration. b. Transfer the Software by assigning the rights under this Agreement to another party, provided that the other party agrees in writing to accept the terms and conditions of this Agreement. In addition, Licensee must ensure that the copyright notice is maintained on the Software transferred. Licensee may not: a. Use the Software, in whole or in part, except as expressly provided in this Agreement. b. Use the Software on more than one workstation at a time. c. Copy, sell, or otherwise transfer the Software or assign its rights under this Agreement, in whole or in part, to another party, except as expressly provided in this Agreement. d. Rent, distribute, license or sublicense the Software. e. Create derivative works based on Software. f. Modify, adapt, translate, reverse engineer, decompile or disassemble the Software. Supplier reserves all rights not expressly granted herein, including, but not limited to, the rights to market the Software either directly or through affiliates, distributors and/or third parties. For further information, please contact your local Roche Applied Science support organization. You will find the contact information on the following webpage: www.roche applied science.com. 3. Limited Warranty The Software is provided “as is” without warranty of any kind, either expressed or implied, including, but not limited to the implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the quality and performance of the Software is with Licensee, should the Software prove to be defective. Licensee assumes the entire costs of all necessary servicing, repair, or correction. However, Supplier warrants that the program media on which the Software is furnished is free from defects in materials and workmanship under normal use for a period of ninety (90) days from the date of delivery as evidenced by a copy of your receipt. SUPPLIER MAKES NO FURTHER WARRANTIES OR GUARANTEES NOR EXPLICIT NOR IMPLIED 12 Cedex Analyzer Operator’s Guide Software License Agreement 4. Disclaimer of Warranties AS FAR AS PERMITTED UNDER THE GOVERNING LAW AS SET FORTH UNDER SECTION 11 OF THIS AGREEMENT THE WARRANTY SET FORTH IN THE PREVIOUS PARAGRAPH, IS IN LIEU OF ALL OTHER WARRANTIES, EXPRESS OR IMPLIED, ARISING BY LAW, FROM A COURSE OF PERFORMANCE, A COURSE OF DEALING, TRADE USAGE, OR OTHERWISE. AS FAR AS PERMITTED UNDER THE GOVERNING LAW AS SET FORTH UNDER SECTION 11 OF THIS AGREEMENT SUPPLIER AND ANY ENTITY CONTROLLING, CONTROLLED BY OR UNDER COMMON CONTROL WITH SUPPLIER (“SUPPLIER’S AFFILIATE”) SPECIFICALLY DISCLAIM, WITHOUT LIMITATION, ALL WARRANTIES OF ANY KIND, WHETHER EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON INFRINGEMENT. SUPPLIER AND SUPPLIER’S AFFILIATES MAKE NO REPRESENTATION OR WARRANTY AS TO THE SOFTWARE OR AS TO THE RESULTS TO BE ATTAINED BY LICENSEE OR ANY THIRD PARTY FROM THE SOFTWARE. LICENSEE ACKNOWLEDGES THAT IT HAS NOT RELIED UPON ANY REPRESENTATIONS OR WARRANTIES MADE BY SUPPLIER OR A SUPPLIER’S AFFILIATE EXCEPT FOR THOSE EXPRESSLY AND SPECIFICALLY SET FORTH IN THIS AGREEMENT. 5. Limitations of Remedies Supplier’s sole liability and Licensee’s sole remedy shall be: a. The replacement of the program media not meeting Supplier’s limited warranty and which is returned to Supplier with a copy of Licensee’s receipt; b. If Supplier is unable to deliver replacement of program media which is free of defects in material and workmanship, Licensee may terminate this Agreement by returning the Software and a copy of Licensee’s receipt to Supplier, and Licensee’s money will be refunded. IN NO EVENT WILL SUPPLIER OR ANY OF SUPPLIER’S AFFILIATES (OR THEIR RESPECTIVE OFFICERS, EMPLOYEES, CONSULTANTS, ATTORNEYS OR AGENTS), BE LIABLE FOR ANY SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, LOST PROFITS, LOST DATA OR INFORMATION, LOSS OF USE OF THE SOFTWARE, BUSINESS INTERRUPTION, LOSS OF BUSINESS REPUTATION OR GOODWILL, OR DOWNTIME COSTS) WHICH THE LICENSEE OR THIRD PARTIES MAY INCUR OR EXPERIENCE, DIRECTLY OR INDIRECTLY ARISING OUT OF OR RELATING TO THE SOFTWARE, THIS AGREEMENT, OR THE TERMINATION OF THIS AGREEMENT, EVEN IF SUPPLIER OR A SUPPLIER’S AFFILIATE HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES AND NOTWITHSTANDING ANY FAILURE OF ESSENTIAL PURPOSE. THE AGGREGATE LIABILITY, ON A COMBINED BASIS, OF SUPPLIER AND SUPPLIER’S AFFILIATES (AND THEIR RESPECTIVE OFFICERS, EMPLOYEES CONSULTANTS, ATTORNEYS, AND AGENTS) FOR DAMAGES FOR ANY CAUSE WHATSOEVER DIRECTLY OR INDIRECTLY RELATING TO OR ARISING OUT OF THIS AGREEMENT OR THE SOFTWARE, AND REGARDLESS OF THE FORM OF ACTION, SHALL BE LIMITED TO, AT SUPPLIER’S OPTION, REPLACEMENT OF THE SOFTWARE OR REFUND OF THE FEES RECEIVED BY SUPPLIER OR A SUPPLIER’S AFFILIATE FROM LICENSEE WITH RESPECT TO THE SOFTWARE. 6. General Information Licensee may not sublicense, assign or transfer the license or the Software, in whole or in part, except as expressly provided in this Agreement. Any attempt otherwise to sublicense, assign or transfer any of the rights, duties or obligations hereunder is void. Prologue 13 Software License Agreement 7. Intellectual Property Rights Licensee shall only hold those rights to the Software that are expressly described in Section 2 of this Agreement. Any other rights with regard to the Software, including without limitation, ownership rights and patent, copyright, trademark, trade secret and other intellectual property rights, shall remain the sole property of Supplier. Licensee will not remove from the Software any references to copyrights, trademarks or other ownership rights, or cover up or alter any such references. Licensee will take all reasonable steps to prevent any unauthorized use, reproduction, sale, or publication of the Software or the unauthorized provision of access thereto. Licensee will indemnify and hold harmless Supplier from any losses, damages, claims and expenses (including, without limitation, reasonable legal expenses) relating to any infringement of the rights of Supplier caused by Licensee, Licensee’s breach of this Agreement or Licensee’s use of the Software in a manner not authorized under this Agreement. 8. Duration and Termination The Agreement is effective until terminated. Licensee may terminate this Agreement at any time by destroying the Software and documentation relating to the Software in any form. The Agreement will terminate automatically and without notice from Supplier, if Licensee fails to comply with any term or condition of this Agreement. Licensee agrees to destroy the Software upon termination of this Agreement by Supplier. On any termination of this Agreement, all rights of use of the Software held by Licensee shall expire. 9. Import, Export and Use of the Software Licensee shall be exclusively responsible for ensuring compliance with the relevant legislation relating to its rights to import, export or use the Software. 10. Miscellaneous Should any part of this Agreement be declared void or unenforceable by a court of competent jurisdiction, the remaining terms shall remain in full force and effect. Failure of Supplier to enforce any of its rights in this Agreement shall not be considered a waiver of its rights, including but not limited to its rights to respond to subsequent breaches. By opening and using this Software Licensee acknowledges that he has read this Agreement, understands it, and agrees to be bound by its terms and conditions. Licensee further agrees that this Agreement is the complete and exclusive statement of the Agreement between Licensee and Supplier and supersedes any proposal or prior agreement, oral or written, any other communications between Licensee and Supplier relating to the subject matter of this Agreement. The headings of the several Sections of this Agreement are intended for convenience of reference only and are not intended to be a part of or to affect the meaning or interpretation of this Agreement. 11. Governing Law and Place of Jurisdiction This Agreement shall be governed by and construed in accordance with the laws of Germany, without giving effect to any choice of law principles thereof. The parties agree that the United Nations Convention on Contracts for the International Sale of Goods (1980) is specifically excluded from application to this Agreement. The parties agree that courts of Mannheim, Germany, shall have exclusive jurisdiction over any dispute arising out of or in connection with this Agreement. 14 Cedex Analyzer Operator’s Guide Preamble IX. Preamble Before setting up operation of the Cedex Analyzer, it is important to read this Operator’s Guide thoroughly and completely. Non-observance of the instructions contained herein or performing an operation not stated in this Operator’s Guide could involve safety hazards. X. Contents of this Operator’s Guide This Operator’s Guide describes the operation of the Cedex Analyzer. It contains the following chapters: Chapter A Overview presents the specifications of the Cedex Analyzer. Chapter B System Description contains the installation requirements of the Cedex Analyzer and a description of the system’s components. This chapter also gives a short overview of the basic functions and operation of the system. Chapter C Operation describes the operating procedures for the Cedex Analyzer, including the correct placement of the reagents and disposables and instructions for carrying out single and multiple measurements of cell samples. Chapter D Software provides a detailed description of the Cedex Analyzer software functions and features. Chapter E Maintenance and Care describes the maintenance and care procedures that are required for the Cedex Analyzer. Chapter F Troubleshooting contains troubleshooting information for the Cedex Analyzer. Chapter G Appendix contains a detailed list of System Options and User Preferences, and an index. XI. Conventions used in this Guide Text Conventions To present information consistently and memorably the following text conventions are used in this Operator’s Guide: Numbered list: Steps in a procedure that must be performed in the order listed. Italic type: Used for operating instructions for the Cedex Software. In addition, important notes and information notes are shown in italic type. Blue italic type: Refers to a different section in this Operator’s Guide, which should be consulted. Prologue 15 FCC Notification Symbols In this Operator’s Guide the following symbols are used as visual signals: Symbol Heading Description WARNING This symbol is used to indicate that non-compliance with instructions or procedures could lead to physical injury or even death or could cause damage to the system. IMPORTANT NOTE Information critical to the success of the procedure or use of the product. INFORMATION NOTE Additional information about the current topic or procedure. Procedure continued on next page. ■ End of procedure. The following symbols appear on the analyzer: Symbol XII. Heading Description CE MARK The CE mark on the analyzer type plate indicates conformity with requirements of the directives relevant for this analyzer. DANGEROUS ELECTRICAL VOLTAGE On the back of the analyzer near the power box. FCC Notification Changes or modifications to this unit not expressly approved by the party responsible for compliance may void the user‘s authority to operate the equipment. Note: This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to Part 15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment. This equipment generates, uses and can radiate frequency energy and, if not installed and used in accordance with the instruction manual, may cause harmful interference to radio communications. Operating this equipment in a residential area is likely to cause harmful interference, in which case the user will be required to correct the interference at his own expense. 16 Cedex Analyzer Operator’s Guide Warnings and Precautions XIII. Warnings and Precautions Moving parts may cause hand injuries. Never use the Cedex Analyzer without the protective cover on the Multi Sampler and Syringe Module. It is important that the following safety instructions and guidelines be observed in order to ensure safe and reliable operation of the Cedex Analyzer: Place the device on a dry and sturdy surface, free of vibrations. Avoid transporting the device as much as possible once it has been assembled. Prevent the device from getting wet. Protect the device from dust and smoke. Do not expose the device to direct sunlight. Ensure there is sufficient air circulation around the Cedex Analyzer during operation (particularly around the computer and monitor). Operate within a constant temperature range of 50°F – 100°F (10°C – 40°C). For best performance, it is recommended to keep the analyzer permanently on and only shut down the software application on a regular basis. The Cedex Analyzer should only be used with the supplied or specified devices (Cedex Analyzer, Cedex Software, monitor, computer, Multi Sampler, Reagent Tray). Do not install any additional software on the corresponding computer. Only trained personnel in a controlled laboratory environment should operate the Cedex Analyzer. All services and repairs should be performed only by authorized service technicians. Always ensure that there are sufficient reagents in the reagent containers. Clean the containers before reusing them. Always observe the safety regulations when handling Trypan Blue, Detergent, Cleaning Solution or acids and bases. Waste contaminated with tissue or cells, e.g., Cedex Sample Cups, pipette tips, etc., must be disposed of according to the recommended rules for handling biohazard materials. Any leaks in the Liquid Management system must be repaired immediately. Contact your distributor or authorized service technician. Always ensure that there is a Cedex Sample Cup attached to the single sample port or placed in the DefaultCup position on the Multi Sample tray. Only use Cedex Detergent for the cleaning process in the Liquid Management system. Only use Cedex Sample Cups from Roche Diagnostics GmbH for the conveyance of cell samples to the sample port. Other sample cups can cause irreparable damage to the Cedex Analyzer! Always wear protective clothing, particularly gloves, when handling samples. To prevent damage to the flow chamber, no particles larger than 80 µm should enter the measurement system. Particles (especially microcarriers) larger than 90 µm should not gain access into the analyzer because they cause irreparable damage and render the device non-functional. Dirt or dust particles should not gain access into the device. Ensure that all equipment required for sample preparation, e.g., Cedex Sample Cups, pipette tips, etc., are stored in a dust-free environment since coarse dust particles can impair the flow chamber’s functionality. Check that the Cedex Sample Cup is free of contamination before use. Only clean Cedex Sample Cups can guarantee optimal functioning of the Cedex Analyzer. Prologue 17 Disposal of the Analyzer Ensure that the Trypan Blue solution is free of contamination, otherwise filter prior to use. Roche Diagnostics GmbH recommends the use of the Cedex Reagent Kit. Secure your measurement data. If the system has been upgraded from some previous version to software version 2.2, it is possible that some default settings in the System Options may have slightly different values than those described in this manual. The settings described in this manual apply to systems on which software version 2.2 has been installed as the original software. The software and hardware of your Cedex Analyzer can differ from the information described here, but this should not make a difference to the operational functions in general. The manufacturer is not responsible or liable for any damages resulting from improper use or failure to comply with the regulations in the Operating Instructions. Electrical Safety The Cedex Analyzer is designed in accordance with Protection Class I (IEC). The chassis/housing of the instrument is grounded to protection earth (PE) by means of a cord. For protection against electrical shock hazards, the instrument must be directly connected to an approved power source such as a three-wire grounded receptacle for the 110 V or 230 V line. Do not use an ungrounded receptacle; have a qualified electrician replace the ungrounded receptacle with a properly (PE) grounded receptacle in accordance with the local electrical code. Do not use an extension. Any break in the electrical ground path, whether inside or outside the instrument, could be hazardous. Under no circumstances should the user attempt to modify or deliberately defeat the safety features of this instrument. If the power cord becomes cracked, frayed, broken, or otherwise damaged, replace it immediately with the equivalent part from Roche Diagnostics. XIV. Disposal of the Analyzer Disposal Recommendations All electrical and electronic products should be disposed of separately from the municipal waste system. Proper disposal of your old appliance prevents potential negative consequences for the environment and human health. The analyzer must be treated as biologically contaminated hazardous waste. Decontamination (i.e., a combination of processes, including cleaning, disinfection and/or sterilization) is required before reuse, recycling or disposal. Dispose of the analyzer according to local and/or laboratory regulations. For more information contact your local Roche Support personnel. Components of your control unit such as the computer, monitor, keyboard, etc. which are marked with the crossed-out wheeled bin symbol are covered by the European Directive 2002/96/EC on waste electrical and electronic equipment (WEEE) of the European Parliament and the Council of January 27, 2003. These items must be disposed of via designated collection facilities appointed by government or local authorities. For more information about disposal of your old product, please contact your city office, waste disposal service or local Roche Support personnel. Disposal Recommendations It is left to the responsible laboratory organization to determine whether control unit components are contaminated or not. If contaminated, treat in the same way as the analyzer. 18 Cedex Analyzer Operator’s Guide A Overview The Cedex Analyzer automatically determines the cell concentration and viability of cell suspensions. The analysis is based on the Trypan Blue Exclusion Method whereby cell suspensions are stained and analyzed. The data obtained allows for the evaluation of the overall state of the cell culture, including the specific growth rate and doubling time of a cell population, as well as the documentation of the cultivation process. A The evaluation of the samples is based on automatically obtained digital images that are analyzed using analysis software on a separate computer (Cedex Control Unit). All the necessary steps – from the staining of the samples to the recording and evaluation of the image data – are automatically performed by the analyzer. Recognition and differentiation of cells as either viable or dead is done under standardized conditions, which provides very precise and objective results. A variety of parameters, including Viable Concentration, Total Concentration, Viability, Total Object Count, Average Compactness and Average Diameter are analyzed using result data from single images, as well as from all of the selected images of a sample. Standard deviation (Std. Dev.) of the number of cells from image to image is also calculated. In addition, the Aggregate Rate, which shows the percentage of the total number of cells that appear in aggregates (clusters), is determined for both single images and all of the images. The use of a Live Operator makes it possible to directly observe the effects on the analysis of a sample when the image analysis software (Operator) is adjusted. Graphical representations of the measurement results can be viewed in the Measurement Statistics Histogram, Diameter Histogram, Compactness Histogram, Aggregate Histogram and Cultivation Time Chart. In the Measurement Statistics histogram, individual images can be compared to give a better overview of the distribution of the cells in the images. The Cell Diameter Histogram shows the diameter distribution of living cells. The deviation of the shape of living cells from that of an ideal sphere is represented in the Compactness Histogram. The Aggregate Histogram provides an overview of the amount and size of aggregation found in the cell culture. The Cultivation Time Chart displays growth curves and cultivation parameters in a time- dependent manner. The results of the Cultivation Time Chart can be separately printed out. For further processing of the results in other programs, data export in formats such as Excel-compatible formats and CSV (Comma Separated Values, generally applicable) is possible. The Cultivation Time Chart includes calculations for the doubling time [T] and specific growth-rate [µ]. The Cedex Software 2.2 can be operated on Windows® XP Professional. Secure data handling, as well as a carefully designed user management system, guarantee compatibility with 21 CFR, Part 11. Access security for the Cedex Analyzer has been stepped up. Access is only allowed for authorized persons. The workstation can be automatically blocked after a certain number of consecutive entries of a false password via the Systems Options. A warning message will appear before the last allowed attempt. Overview 19 Description of the Cedex System A 1 Description of the Cedex System The Cedex System consists of two functional units, the Analyzer (see Figure 1) and the Control Unit (computer equipped with the Cedex Software 2.2). Preparation and processing of the samples takes place in the analyzer. The analysis software is installed on a computer and controls the analyzer, as well as the analysis and evaluation of the images obtained. Syringe module with 8-way valve sample port with Cedex Sample Cup 2.5 ml syringe switch ON/OFF tray with 5 reagent containers (from left to right: Trypan Blue, Detergent, Cleaning Solution, distilled or deionized water, waste) Figure 1: The Cedex Analyzer The Analyzer consists of two main components, the hardware for image capturing and the Liquid Management system. The flow chamber is specially developed to allow for the analysis of a defined volume of cell suspension. The Liquid Management system is responsible for staining the sample as well as for filling and cleaning the flow chamber and liquid feed system. The volumes of sample and dye, as well as specific cleaning solutions required for each cleaning routine, are precisely controlled via the syringe module with the 8-way distribution valve. The individual components of the Liquid Management system are easily accessible to allow for trouble-free maintenance and control. 20 Cedex Analyzer Operator’s Guide The Measurement Procedure The Trypan Blue Exclusion Method 2 The Measurement Procedure The determination of the number of viable cells (cells/ml) and viability of cell suspensions (the percentage of viable cells from the total cell sample) is a fully automated, standardized procedure based on the manual Trypan Blue Exclusion Method. A defined volume of Trypan Blue is added by the syringe to the Cedex Sample Cup containing the cell suspension. The cell suspension and dye are optimally mixed between the syringe and Cedex Sample Cup by controlled pump actions and then incubated for exactly same amount of time for each measurement. This minimizes effects on the viability measurements that might be caused by the toxicity of the Trypan Blue. A After the incubation period, the stained cell suspension in the syringe is then transported in small portions through the capillary tubes and 8-way valve to the flow chamber. A set number of microscopic images of the cell sample is taken in the flow chamber and transferred to the analysis software via an integrated interface in the measurement system. Once the measurement procedure is completed, a cleaning routine is automatically performed by the Liquid Management system. It is only possible to begin a new measurement after the cleaning routine has finished. 2.1 The Trypan Blue Exclusion Method The Trypan Blue Exclusion Method is based on the principle that viable cells will not take up the dye, while dead or dying cells have a compromised membrane that allows for the uptake of the dye. Thus, dead cells will appear darkly stained in a microscope. Trypan Blue has a greater affinity for serum proteins than cellular proteins. If the microscopic image has a dark background due to high quantities of stained serum proteins, centrifuge the cell sample and re-suspended it in a protein free-medium or physiological saline solution prior to counting. Overview 21 Data Analysis A 3 Data Analysis The analysis software and its graphical user interface (GUI), known as the Cedex Control Center, enables the user to work with the Cedex Analyzer. The image analysis software (Operator) recognizes structures and identifies particles, thus differentiating cells from cell debris and dirt particles. Live and dead cells are differentiated according to their degree of Trypan Blue staining. Image processing is integrated in the Cedex Control Center in such a way that the user or Administrator can check on its function in the system. The analysis process cannot be altered during data recording in order to allow for consistent and objective measurement results. 22 Cedex Analyzer Operator’s Guide Technical Specifications of the Analyzer 4 A Technical Specifications of the Analyzer Cedex Analyzer Method of measurement Digital image and pattern recognition Viable/dead cell differentiation Trypan Blue Exclusion Method Detectable cell concentration range 5 × 104 – 1 × 107 cells per ml Detectable cell diameter range 8 µm – 40 µm Required sample volume 1000 µl Average measurement period < 4.0 min Geometric resolution 2.08 µm/Pixel Chamber height 100 µm Material and diameter of the capillaries Teflon, 765 µm Operating temperature +10°C to + 40°C (Optimal image quality is achieved between 20°C and 30°C) Maximum temperature change 5°C per hour Maximum humidity deviation 5% per hour Operating humidity 20% – 80% relative humidity (non condensing) Pollution Degree 2 (according to IEC 61010-1) Dimensions Height: 660 mm (26.0 inches) Width: 300 mm (12.0 inches) Depth: 600 mm (23.6 inches) Weight without Multi Sampler: 33.0 kg Energy requirements 100 – 250 VAC, 50 – 60 Hz Energy consumption 24 VDC 2.0 A Installation Category II (according to IEC 61010-1) Overview 23 Technical Specifications of the Analyzer A Multi Sampler MS20C (optional) Number of samples 1 – 20 Average measurement period for 20 samples (20 images per sample) < 90 min Dimensions Height: 250 mm (9.84 inches) Width: 250 mm (9.84 inches) Depth: 190 mm (7.48 inches) Total Weight: 5.2 kg (11 Ibs.) Energy requirements 24VDC, 9A DC Energy consumption max. 30W Power supply Input: 100 – 240 VAC, 47 – 62 Hz Output: 24VDC Hardware Requirements for the Cedex Control Unit Computer x86-Architecture, Intel Pentium IV, Minimum 2 GHz required 3 GHz recommended Operating system Windows® XP Professional RAM Minimum 512 MB RAM Recommended 1 GB RAM Hard-disk storage 100 MB free hard-disk storage for installation of application Minimum 20 GB free hard-disk space for data storage of approx. 1000 measurements Recommended: 80 GB Serial ports minimum 2 free ports (minimum 3 free ports if MS20/AS20 installed) Frame Grabber Eltec PC-eye 4 CD/DVD burner Minimum CD burner required DVD burner recommended if the computer will not be connected to a server 24 Graphic card Resolution: 1024 × 768 Pixel, 24-bit color Monitor (color monitor or -TFT) 1024 × 768 Pixel, 24-bit color Cedex Analyzer Operator’s Guide Installing the Cedex System B System Description 1 Installing the Cedex System The Cedex System comprises the Cell Analyzer and the Control Unit (PC equipped with the Cedex Software 2.2). The Cell Analyzer and Control Unit are delivered and assembled by a service technician authorized by Roche Diagnostics GmbH. The service technician assembles the Cell Analyzer. He/she controls the installation, activates the security settings, runs the focus adjustments and ensures that the Cedex Analyzer is operational. Finally, he/she will create a report on the installation and current status of the device. We recommend choosing your local IT specialist as the system administrator for the general administration of the Windows operations. This person controls the configurations that regulate system access at the level of the operating system. B Installation of the Cedex Analyzer is done in the following steps: The system administrator should set up net access and/or printer installation, if desired, before the service technician assembles the Cedex Analyzer. The Cedex Analyzer is assembled by a service technician authorized by Roche Diagnostics GmbH. The service technician installs the Analyzer and checks the security settings in the software. The service technician will check the software information, perform a focus adjustment and ensure that the Cedex Analyzer is ready to use. Finally, he/she will create a current status report of the device. The system administrator is responsible for setting up the user accounts for the operating system. The system administrator is also responsible for ensuring data safety and security of the system. The Administrator for the Cedex Analyzer then sets up Cedex System user accounts and assigns them the required rights (see “Administration of User Accounts”). Please be aware that the correct operation of the analyzer and software can only be guaranteed if no other software has been loaded on to the computer. The software and hardware of your Cedex Analyzer may differ from the information described here, but this should not make a difference to the operational functions in general. System Description 25 Choosing a Suitable Location Connecting or disconnecting the device 2 Choosing a Suitable Location The Cedex Analyzer is highly sensitive and consists of top-quality electronic and optical components. To guarantee optimal and reliable performance of the Cedex Analyzer, select the appropriate location in accordance with the safety regulations described in the Prologue. Avoid further transportation of the Cedex Analyzer after the professional installation. B Vibrations or shaking must be avoided when operating or transporting the analyzer over short distances. Focus adjustment must be done after transportation (see “Automatic Adjustment”). Injury from heavy loads The Cedex Analyzer weight is 33 kg. (72.6 lbs). No attempt should be made by the user to remove or set up the instrument alone. You may injury your hands, fingers, or back when putting the analyzer in place. 2.1 Connecting or disconnecting the device First connect the device using the power cord to the external power supply. A blue power switch is located on the front panel of the Cedex System. When the switch is turned to ON it illuminates, indicating that the device is alive. In case of problems, turned the device switch to OFF. In case of emergency, remove the power line from the Cedex System immediately switch ON/OFF Figure 2: The ON/OFF switch for the Cedex Analyzer 26 Cedex Analyzer Operator’s Guide Connecting Hardware Components 3 Connecting Hardware Components Follow the instructions below to connect the hardware components (see Figure 3 and Figure 4 below): 1 Connect monitor, keyboard and mouse to their respective ports on the PC. 2 Connect one end of the video cable to the Video port of the measurement system. 3 Connect the other end of the video cable to the Video port of the PC. 4 Connect one end of the first serial cable to the Focus port of the measurement system. 5 Connect the other end of the first serial cable to the Focus port of the PC. 6 Connect one end of the second serial cable to the Syringe port of the measurement system. 7 Connect the other end of the second serial cable to the Syringe port of the PC. B ■ Check that your connections are correct otherwise an error message will appear: “Error: HWManager Pump connection failed” or “Error: Device Pump is not connected”. Figure 3: Cedex Analyzer connections Figure 4: PC connections Connect the measurement system, PC and monitor to the main power supply with the cords enclosed. Check the technical data. System Description 27 Connecting Hardware Components Completing the Windows Mini-setup 3.1 Completing the Windows Mini-setup When starting the Cedex Control Unit for the very first time, a Windows mini-setup may run. The setup allows the user to tweak the final settings of the new system (e.g. selection of time zone, keyboard etc.). The mini-setup dialogs should be self-explanatory. The following list provides some additional information to get through the process. Note that the order of screens may be different and some topics may not appear on your system: B Roche technical services strongly recommends not changing the regional settings. Changes in the regional settings may result in problems with date and time format within the Cedex Software. You may be required to enter the 25-digit product code. It is located on the Control Unit. Protect your PC: Roche technical services recommends turning on automatic updates if the Control Unit is permanently connected to the internet via a LAN. Otherwise, click no, not right now. Computer name: The Control Unit name has already been set to a unique name. However, your company might enforce a different naming convention. If you are not sure, leave it as it is. The name can be changed at any time later on. Computer description: This is a purely informational field that helps to identify the Control Unit in a network. You may want to enter a short descriptive text. Again, this setting can be adjusted later. If asked to choose an Administrator account password, be sure to make a note of the password and store it in a safe place. If asked to choose whether to add the computer to a domain, Roche technical services recommends choosing No. Your local network policy may require a different strategy, but you are free to join a domain any time later on. Register with Microsoft: It is not necessary to register your Windows copy with Microsoft, so No can be safely chosen. Note that registration is not activation (see below). Internet account setup: The operating system has been configured for access to the Internet over a Local Area Network (LAN). Roche technical services recommends clicking No and proceeding to the next step. When the mini-setup has finished, the Control Unit will automatically restart and present the login screen after a short while. Some Control Units may require immediate Windows activation. Follow the instructions on the screen. Roche technical services recommends activation over the internet if the Control Unit is already connected to a LAN. However, it may be necessary to activate Windows XP via telephone if the Control Unit is not yet connected to the internet. 28 Cedex Analyzer Operator’s Guide Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Installing the Cedex Software 2.2 4 Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 The Cedex Software 2.2 is pre-installed on the Control Unit delivered with the Cedex Standard System. This chapter provides instructions for installing the Cedex Software 2.2, should it be required. In addition, instructions are provided for updating older Cedex Software 2 versions to Cedex Software 2.2. 4.1 Installing the Cedex Software 2.2 Before carrying out any form of installation or update procedure, the actual (effective) values for the FlowFactor and ChamberHeight must be noted down and stored for future reference! These values may need to be adjusted in the System Options after the installation or update procedure is complete. The value for FlowFactor is located in the System Options menu under the General tab. The value for the ChamberHeight is located in the System Options menu under the Hardware tab. See the chapter “System Options and User Preferences” in the Appendix for more information. B The Cedex Software 2.2 must be installed from a Windows account with administrator privileges (e.g. WinAdmin, see “Securing Access Rights”) The Cedex Software 2.2 requires a Firebird database server, which is installed automatically during the setup process. To install Cedex Software version 2.2, do the following: 1 Run the Cedex 2.2.1.exe from the install CD by double-clicking on it. 2 A window will open asking for confirmation of the installation of the Firebird database software: Figure 5 3 Confirm the dialog with OK. The Firebird database software will be installed or updated: Figure 6 System Description 29 Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Installing the Cedex Software 2.2 4 B After completion of the installation of the Firebird database software, the setup will ask for confirmation of the installation of the .Net Framework: Figure 7 If an older Cedex Software version 2.x is installed on the Control Unit, the confirmation dialog shown in Figure 6 will not appear. Instead, the following window will appear: Figure 8 If this occurs, proceed according to the directions in the chapter “Updating Older Cedex Software version 2.x to Cedex Software 2.2”. 5 Click on Next in the Setup window shown below Figure 9 6 Check the I Agree box then click on Next in the License Agreement window shown below: Figure 10 30 Cedex Analyzer Operator’s Guide Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Installing the Cedex Software 2.2 7 The Installations Settings window will appear. Select Cedex Server and Cedex Client, then click on Next. B Figure 11 8 In the Installation Folder window that appears, choose the folder recommended by the program. Ensure that the option Install Cedex 2.2 for Everyone is selected, then click on Next. Figure 12 9 In the following window, click on Next to start the installation: Figure 13 System Description 31 Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Installing the Cedex Software 2.2 10 A window showing the progress of the installation will appear as shown below: B Figure 14 11 During the installation, the following Cedex 2.2 Configuration window will appear: Figure 15 To continue with the installation, certain actions must be carried out in this window: 1) a password for the Database User must be entered, 2) the serial number of the Cedex Analyzer must be entered, and 3) the system settings must be verified. Do the following: a. Enter “cedex” as the password for the database access (a database user, CEDEXUSER, is automatically created with that password). Write down the password for future reference! b. Enter the serial number of your Cedex Analyzer. c. Verify the Cedex System Type in the Cedex System identification group box. d. Uncheck the “use Auto/Multi Sampler AS20/MS20” checkbox if you don’t have a Multi Sampler. e. Enter a description of your system in the Cedex System identification group box. 12 After completing all steps in the Cedex 2.2 Configuration window, the Next button will become active. Click on the Next button to continue the installation. Figure 16 32 Cedex Analyzer Operator’s Guide Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Installing the Cedex Software 2.2 13 After installation of the software, the Installation Complete window will appear. Click on Close to confirm. B Figure 17 14 The Setup Succeeded window will appear if the installation was completed successful. Confirm with OK. Figure 18 15 Test and Archive certificates are automatically installed into the “Trusted Root” certificate store during setup. ■ 4.1.1. Setting the Cedex Server to Autostart The Cedex Server must be started before the Cedex Client software can be started. If desired, the Cedex Server can be configured so that it starts automatically when the Control Unit is turned on. To configure the Cedex Server to autostart, do the following: 1 Open a Windows explorer window by right-clicking with the mouse on the Windows Start button and selecting Open All Users. 2 Copy the shortcut Cedex Server from the Start menu Programs/Cedex 2.2 to the Startup folder (found in the Start menu under Programs/Startup). 3 Open the properties window for the Cedex Server by right-clicking on the icon and selecting Properties. Select the Shortcut tab and change the property for Run to Minimized via the drop-down menu. ■ System Description 33 Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Starting up the Software 4.2 Starting up the Software Once the installation of the software is complete, the software can be started and final adjustments made. Do the following: B 1 Start Cedex Server first (if the Cedex Server has not already automatically started), then start the Cedex Client. 2 Windows Security Alert may possibly ask whether the programs CedexServer and GUI should be blocked. If this occurs, press the Unblock button for each. 3 Log in as SuperUser (password: spass). 4 Confirm the empty reagent container warnings. 5 If there is a message that hardware components could not be found at the configured serial ports, terminate the Cedex Client and the Cedex Server after the message Hardware startup completed appears, and restart the software as described in step 1, above. 6 Verify that the system is not running in demo mode (i.e. make sure there is no Demo label visible in the Cedex Control Center). 7 Open the Diagnosis window via the Setup menu of the Cedex Control Center and verify the configuration of the system. For a Cedex Analyzer with Auto Sampler or Multi Sampler there must be a module AS20Port. 8 Each Cedex Analyzer has a few unique specifications related to the particular flow chamber that has been put in. These numbers must be verified and/or adjusted in the System Options window before measurements can be run. Verify and/or make the following changes in the System Options window under either the General or the Hardware tabs: a. Verify MultiSamplerPresent (0 = Single Port, 1 = Auto/Multi Sampler) in the Hardware tab. b. Enter the appropriate value for the ChamberHeight in the Hardware tab. c. Enter the appropriate value for the FlowFactor in the General tab. 9 Replace or refill the Reagent Kit containers. See “Preparing the Analyzer for Measurements”. 10 Carry out a Prime. 11 Carry out an automatic adjustment via the Automatic Adjustment window in the Functions menu. ■ The Cedex Analyzer is now ready to use. 34 Cedex Analyzer Operator’s Guide Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Updating Older Cedex Software version 2.x to Cedex Software 2.2 4.3 Updating Older Cedex Software version 2.x to Cedex Software 2.2 4.3.1. Overview Before starting an update of your current Cedex Software 2 installation to Cedex Software version 2.2, ensure that: You have Administrator access to the Control Unit. The Firebird database password (i.e. of the SYSDBA account) is available in case it has been changed, e.g. because the installation has been made 21 CFR Part 11 compliant. A storage device with enough disk space is available for a backup of the current installation. Check the size of the folder containing all Cedex Software 2 files, including the database file (usually the directory C:\Cedex2). The size of the backup will be approximately the size of this folder. Enough time is scheduled for a backup of the current installation (approximately one hour for backup to a fast external hard drive per 10 GB disk space used in the Cedex2 directory, including the database file). 4.3.2. B Updating to Cedex Software 2.2 Make sure that you have created a backup of the Cedex Database and that you have fully read and understood the following instructions before proceeding with the update of the Cedex Software! If an error occurs or if you do something wrong, this could result in data loss and/or could prevent the Cedex Software 2.2 from operating! 1 Run the Cedex 2.2.1.exe from the install CD by double-clicking on it. 2 If the Firebird database software is not up to date, the following dialog will appear: Figure 19 Should the dialog appear, confirm it with OK to update the Firebird database software: Figure 20 System Description 35 Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Updating Older Cedex Software version 2.x to Cedex Software 2.2 3 B After the update of the Firebird database software has finished, the following main dialog will appear: Figure 21 If an older Cedex Software version 2.x is not installed on the Control Unit, the confirmation dialog shown in Figure 21 will not appear. Instead the following dialog will appear: Figure 22 Should this occur, proceed according to the instructions in the chapter “Installing the Cedex Software 2.2” and “Starting up the Software”. 4 By default, Cedex Software version 2 is installed under the directory C:\Cedex2. If your software was installed under another directory, the field under the Cedex 2 directory line must be changed to the appropriate directory. Change the entry in this field by clicking on the change button next to Cedex 2 directory field. 5 By default, the location of the Cedex Software database file is C:\Cedex2\DB\CEDEX.FDB. If the database file is in a different location, the field under to the Cedex 2 directory must be changed to the appropriate pathway. Change the Cedex 2 database file if it is not C:\Cedex2\DB\CEDEX.FDB by clicking on the change button next to Cedex 2 database file. 6 If the password of the Firebird database administrator SYSDBA has been changed (e.g. because the system has been made 21 CFR Part 11 compliant), uncheck use standard SYSDBA password (“masterkey”). In this case, the database password will be requested just before the update is carried out. To create the backups successfully, it is necessary that the user account used for updating has read access to the Cedex2 directory and Cedex Database file. Verify the backup files before proceeding with the update! 7 Click on the Create backup of current installation button (see Figure 21) and select the destination directory for the backup by clicking on the OK button. A Browse window will appear in which the destination directory can be selected, as shown below: Figure 23 36 Cedex Analyzer Operator’s Guide Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Updating Older Cedex Software version 2.x to Cedex Software 2.2 8 In the next window, check that the source directory/database file and destination (backup) directory settings are correct. If correct, click on the Yes button to start the backup. Figure 24 9 The backup process may take from several minutes up to hours depending on the size of the installation and the read/write speed of the backup media. A file copy dialog will show the backup progress: B Figure 25 10 After successful backup of the installation, the message below will appear. Confirm by clicking on the OK button: Figure 26 11 The update process can now be started. Click on the Update current installation to version 2.2.1 button as shown below: Figure 27 12 If you unchecked the use standard SYSDBA password (“masterkey”) checkbox in step 6, enter the database of the Firebird SYSDBA account and click on the OK button as shown in the figure below: Figure 28 13 A backup reminder and warning will appear that must be confirmed by clicking on the YES button: Figure 29 System Description 37 Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Updating Older Cedex Software version 2.x to Cedex Software 2.2 14 Check the I Accept box then click on Next in the License Agreement window shown below: B Figure 30 15 A Cedex Job Runner window that provides a protocol of the update process will open. At the end of the update, a success message should appear. Confirm by clicking on the OK button: Figure 31 16 Verify that there are no errors or exceptions displayed in the Cedex Job Runner window. If any errors or exceptions appear, please contact your local Roche technical services. ■ The Cedex Software version 2 installation is now updated to version 2.2. 38 Cedex Analyzer Operator’s Guide Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Updating Older Cedex Software version 2.x to Cedex Software 2.2 4.3.3. Restoring a Cedex Software 2 Backup This procedure should only be carried out in case a failure occurs during installation of the Cedex Software 2.2 update as described in “Updating to Cedex Software 2.2”. Carry out this procedure only after consultation with Roche technical services! If you choose to restore the backup, all data stored in the current database will be overwritten by the data stored in the backup database! This means, for example, all measurements and all configuration changes carried out on the system after the original backup was made will be lost, even if the measurements have been archived or exported. Carry out the following steps to restore the Cedex Software 2 backup that was created in step 7 in the chapter “Updating to Cedex Software 2.2”: 1 Locate the active Cedex2 folder on the hard disk. It is usually located at C:\Cedex2, which is the default location selected during installation. Delete the Cedex2 folder by right clicking on it and selecting Delete: B Figure 32 2 Confirm the upcoming message by clicking on Yes: Figure 33 3 Locate the folder where the backup of the Cedex2 folder and database has been stored. Copy that folder by right clicking on it and selecting Copy: Figure 34 System Description 39 Installing Cedex Software 2.2 or Updating to Cedex Software 2.2 Updating Older Cedex Software version 2.x to Cedex Software 2.2 4 Navigate to the location from which the Cedex2 folder was deleted in step 1 (usually C:\). Paste the backup in this location: 5 The Cedex2 folder will be copied: B Figure 35 Figure 36 6 Verify that the backup Cedex2 folder is placed in the location where the folder deleted in step 1 was located (the directory should usually be C:\Cedex2). 7 (optional) If the active database file is located in a folder different from the DB subfolder contained within the Cedex2 folder, locate the database file (name: CEDEX.FDB) in the folder where the backup of the Cedex2 folder and the database has been stored. Copy it to the location of the original database file, overwriting the existing one. 8 Verify that the Cedex Software 2 installation is working as expected. ■ 40 Cedex Analyzer Operator’s Guide Starting the Cedex System after installation 5 Starting the Cedex System after installation The hardware components of the Cedex Analyzer must all be switched on before the analysis software can be started, otherwise the software will not be properly initialized. After the initial installation, switch on the individual devices in the order given below: 1 Switch on the Cedex Analyzer. 2 Switch on the monitor and the PC. The first time the computer is started, a registration window for access at the operating system level will appear. Follow the instructions to register with Windows. ■ System Description B 41 Securing Access Rights Access Control at the Windows Operating System Level B 6 Securing Access Rights 6.1 Access Control at the Windows Operating System Level We recommend choosing your local IT specialist as the system administrator for the general administration of the Windows operations. This person should undertake the configuration of the settings that regulate access to the system at the operating system level. One default user at the operating system level has been factory installed: The Win-Admin user (default password Win-Admin) acts as system administrator for the operating system and has full access to all elements on the desktop including the ability to add/delete programs. 6.2 Access Control at the Cedex System Software Level To launch the software, do the following: 1 Check that the Cedex Server software has already been automatically started (it may appear as a minimized window in the task bar at the bottom of the computer screen). If it has not automatically started, start the server by double-clicking on the Cedex Server icon on the desktop. 2 Start the Cedex Software 2.2 by double clicking the Cedex Client icon on the desktop (the Cedex Server must be successfully launched before the Cedex Client can be started). The Log In window of the Cedex System will open. 3 Enter the username password in the respective fields. By default, the following users are available after installation: a. Superuser (password spass) b. Administrator (password apass) ■ For the Cedex Software, there should generally be at least three levels of users. In addition to normal Cedex System users, who will only use the Cedex System for carrying out measurements, both a Cedex System Superuser and an Administrator should be appointed. The Cedex System Superuser assumes the main responsibility of handling the Cedex System, whereas the Administrator creates and administers user accounts. For security reasons, both the Administrator and the Superuser should protect their access to the Cedex Software 2.2 with new passwords after initial installation. Follow the instructions below to secure access and define a new password: 1 Log in as Administrator or Superuser. 2 Click on the System menu in the Cedex Control Center. 3 Click on Change own password. The Change Password window will appear. 4 Enter the old password first. The new password needs to be entered twice. 5 Confirm by pressing OK. ■ After logging in, users can change their own passwords at any time by following the same procedure. After installation, the user Administrator should set up regular user accounts and provide the necessary rights before regular users run measurements (see “Administration of User Accounts”). For security reasons, the Cedex System Administrator is generally only accorded administrative rights and cannot carry out, reprocess or view measurements. 42 Cedex Analyzer Operator’s Guide Overview of the Cedex Control Center Menu Bar C Operation 1 Overview of the Cedex Control Center The Cedex Control Center is divided into three elements: Menu bar Shortcuts area Event window detailing status of events carried out by the analyzer A description of the individual areas is given below (see Figure 37): C Figure 37: The Cedex Control Center 1.1 Menu Bar The menu bar at the top of the Control Center has 7 menu items: System menu Measurements menu Functions menu Reports menu Master Data menu Setup menu Help menu 1.2 System Menu The menu items have the following functions: Exit: exits the Control Center. Logout: for logging out of the Control Center. Change own password: for changing the password of a user who is logged in. Lock – Unlock System: for automatically or manually locking and unlocking of the system with regard to running measurements. Operation 43 Overview of the Cedex Control Center Measurement Menu 1.3 Measurement Menu The individual menu items have the following functions: Measurement List: This provides a list of the measurements that have been run. Measurements can be sorted or filtered using specific criteria and then viewed (see “Using the Measurement List”). Single Measurement: Selecting this menu item will open a new window in which single measurements can be run (see “Opening the Measurement window and specifying the Operating Mode and Sample Data”). Multi Run: Selecting this menu item will open a new window in which multiple measurements can be run (see “The Multi Run Data Entry Window”). Cultivation Time Chart: This opens a new window in which multiple measurements can be analyzed in a graph form (see “Cultivation Time Chart”). C 1.4 Functions Menu Clicking on the items in the Functions menu will open windows with the following functions: Reagent Kit Status: This window shows the percent of each reagent left. Confirmation of a reagent change is also executed via this window. Operational Data: The operating hours, number of measurements and liquid consumption are tracked in this window. Cleaning Routines: Various cleaning routines can be run using this window. Syringe Maintenance: Used for preparing the syringe for removal and installation. Hardware Management: Prime and shutdown of the Liquid Management, as well as start-up and shutdown of the hardware, are executed in this window. Automatic Adjustment: An automatic focus adjustment is run in this window. SST: This opens a window in which System Suitability Tests (SST) can be set up and executed. The status of SSTs are also displayed. Scheduling: Automatic Prime, LM Shutdown and cleaning routines can be scheduled in this window. Export to File: Measurement results can be exported into various formats, including Excel, from this window. Data Exchange: Data can be imported or exported from the database of one system to the database of another system using these windows. Archiving: Data from the database can be archived or restored in these windows. 44 Cedex Analyzer Operator’s Guide Overview of the Cedex Control Center Reports Menu 1.5 Reports Menu Reports can be generated using this menu for the following types of information: Operational Data Measurement Data System Configuration Parameters Audit Trail Report about the Multi Run Automatic Adjustment and Alignment Verification 1.6 Master Data Menu The menu items have the following functions: Reagent Container Configuration: This window allows the user to set the minimum and maximum vol- umes for the reagents, as well as to set the volumes for the warning and lock levels. User Preferences: The user preferences for default parameters such as measurement parameters, C measurement lists and Cultivation Time Chart can be individually set using this window. Cell Type List: This allows for the creation of customized Cell Types. 1.7 Setup Menu Clicking on these menu items will open up windows with the following functions: Audit Trail: Opens a window that tracks all actions of the system. System options: Various system parameters can be changed by the Superuser using this window. User and Rights Management: The Administrator can create new users and administer their rights in this window. Diagnosis: At the request of Roche technical services, a diagnosis of the entire system can be run with the options listed in this window. Trace and Logging: At the request of Roche technical services, logs of various functions of the system can be created in this window. Report Templates: Report templates can be created using this window. Operation 45 Overview of the Cedex Control Center Help Menu 1.8 Help Menu The Help menu provides general information about the analysis software. 1.9 Shortcuts Area Several buttons that act as short-cuts to certain functions are available in this area, including: List: Opens the Measurement List window. Measure: Opens the Measurement window for running a single measurement. C Multi Run: Opens the Multi Run window for running multiple measurements. CTC: Opens the CTC Views window for setting up Cultivation Time Charts. SST: Opens the System Suitability Test List window for setting up and executing SSTs. Clean: Opens the Cleaning window. HWM: Opens the Hardware Management window Log Out: Logs the user out of the Cedex Control Center. 1.10 Tracking of Status of Events Carried out by the Analyzer In the Event window below the Shortcut area, the status of events that have been carried out by the analyzer is tracked. If, for example, a cleaning routine is run, the completion of the routine will be noted in this window. Previous events can be looked at by using the scroll bar on the right. The window is cleared each time the software is shut down. 46 Cedex Analyzer Operator’s Guide Preparing the Analyzer for Measurements Switching on 2 Preparing the Analyzer for Measurements 2.1 Switching on Each element is switched on separately as follows: 1 Switch on the Cedex Analyzer. 2 Switch on the Multi Sampler (optional). 3 Switch on the monitor and the PC. ■ Cedex Analyzer hardware components must be switched on before starting the analysis software. Otherwise, the analysis software may not be correctly initialized. 2.2 Logging in at the Computer Operating System Level A prompt for a username and password will appear on the computer when everything has been turned on correctly. The user should log in as Win-Admin, password Win-Admin unless a different Windows operating system account has been set up. 2.3 C Starting the Cedex Software 2.2 To launch the software, do the following: 1 Check that the Cedex Server software has already automatically started (it may appear as a minimized window in the task bar at the bottom of the computer screen). If not, start the server by double-clicking on the Cedex Server icon on the desktop. 2 Start the Cedex Software 2.2 by double clicking the Cedex Client icon on the desktop (the Cedex Server must be started before the Cedex Client can be started). The Log In window of the Cedex Analyzer program will open. 3 Enter the username and password (if a password is required) in the respective fields. Factory installed default user is Superuser (password spass). 4 If you are logging in for the first time under a new username, you might be forced to change your password. 5 Click on the OK button to log in or press . The Cedex Control Center appears after a successful login. ■ The user may be prompted to create a new password the first time the Cedex Software 2.2 is started. This serves the purpose of replacing the temporary password given to the user by the Administrator when the user account was created. Follow the program instructions or see “Changing own Password“. The Administrator, Superuser or regular user has access to the assigned functions once he/she has logged into the Cedex Control Center. The regular user only has access rights to routine operations depending on the configurations set by the Administrator. Access rights may vary according to options chosen for each user account. Operation 47 Preparing the Analyzer for Measurements Performing a HW Startup and Prime 2.4 Performing a HW Startup and Prime Two elements of the analyzer are usually shut down at the end of the day: the Hardware Management and the Liquid Management. When the Hardware Management is shut down, several elements of the analyzer, such as the Multi Sampler and pump, are not yet initialized. A HW Startup will initialize hardware interfaces and must be done before a measurement can be performed. If a measurement is attempted before the Hardware Management has been started, an error message will appear, “Cannot start a new process: Hardware Management is not started”. The HW Startup may be automatically carried out when the software is launched if the Administrator has set this up in the system options. C In the case of the Liquid Management, the capillary tubes and syringe are filled with air or water when the analyzer is first installed or any time an LM Shutdown has been performed (see, “Carrying out an LM Shutdown and HW Shutdown”). Performing a Prime will fill the capillary tubes and 8-way valve with the appropriate reagents. All measurements are based on the capillary tubes having a precise amount of reagents in them. Not performing a Prime will lead to cell samples being incorrectly stained and, consequently, inaccurate measurement results. A Prime must, therefore, be performed after an LM Shutdown has been executed in order to run a measurement. Since LM Shutdown should be run at the end of the previous day, a Prime is necessary prior to the first measurement of the day. No measurement is possible without performing a Prime first. If a measurement is attempted before the machine has been primed, an error message will appear, “Cannot start new process: system is not primed”. Both the HW Startup and the Prime functions are located in the same window. Follow the instructions below to perform a HW Startup and Prime: 1 Click on the HWM button in the Cedex Control Center or else select Hardware Management under the Functions menu. The Hardware Management window will open. 2 If the Hardware Management has not been started, the current status field will have the message “HW not started and LM not primed”. 3 Click on HW Startup if required. The Hardware Management will start and the current status field will have the message “HW started and LM not primed”. 4 Ensure that a Reagent Kit is installed (see “Preparing the Reagent Kit”) and a clean, empty Cedex Sample Cup is correctly attached to the sample port or correctly positioned on the Multi Sample Tray, if present (see “The Multi Sampler DefaultCup”). 5 Click on Prime. The duration of a Prime procedure is displayed in the Estimated total time area. The time displayed is an estimate based on the time required for the previous Prime. The message “HW started and LM primed”, appears in the current status field when the Prime has been completed. 6 Click on to close the window. ■ There should not be a break of more than 2 hours between a Prime and a measurement. If more than 2 hours have passed since the last measurement, a new Prime must be performed. 48 Cedex Analyzer Operator’s Guide Preparing the Analyzer for Measurements Preparing the Reagent Kit 2.5 Preparing the Reagent Kit To ensure optimal performance, the reagents must be free of impurities such as dust, crystals, biological material or fluff. The Roche Diagnostics GmbH Cedex Reagent Kit guarantees optimal handling with the best possible safety. One Reagent Kit pack is sufficient for approximately 100 measurements, including the standard cleaning routines. 2.5.1. Installing or Changing the Reagent Kit Proceed as follows to install or change the Reagent Kit: 1 Perform an LM Shutdown if the Liquid Management system has been primed (see “Carrying out an LM Shutdown and HW Shutdown”). 2 Open the new Reagent Kit and place the Reagent Kit containers in the appropriate positions on the reagent tray (see Figure 38). 3 Fill the water reagent container with distilled or de-ionized water. 4 Empty, clean and replace the waste container. 5 Connect the capillaries to the reagent bottles through the holes in the lids. Ensure that the capillary tubes are not bent and almost reach the bottom of the containers. Use the lids to close the reagent containers to avoid dirt-particles getting into contact with the reagents. C The tubes should not be shortened under any circumstances! 6 Remove the lid of the waste container and ensure that the silicone and capillary tubes only reach about 1 cm into the container. 7 Select the Reagent Kit Status option in the Functions menu of the Cedex Control Center. The Reagent Kit Status window will open. 8 Click on the Replace all containers button in right-hand corner of the Reagent Kit Status window to confirm the changing of the Reagent Kit (see Figure 39). The Reagent Control display at the bottom righthand corner of the Cedex Control Center will turn from red to green and indicate the number of runs left. 9 Attach a clean Cedex Sample Cup to the sample port (see Figure 40) or place it in the DefaultCup position on the Multi Sample tray (see “The Multi Sampler DefaultCup”). 10 Click on Prime in the Hardware Management window. ■ Operation 49 Preparing the Analyzer for Measurements Preparing the Reagent Kit Waste container Container for distilled or de-ionized water Container for Cleaning Solution Container for Detergent Container for Trypan Blue C Figure 38: Position of the Reagent Tray with the individual containers Figure 39: Confirming change of the Reagent Kit For reliable functioning of the reagent control (correct number of possible measurements, or reporting an impending overflow of the waste container), it is critical that all of the reagent containers are correctly filled to the line with the appropriate liquid or, in the case of the waste container, completely emptied (see “Refilling Containers Individually”). The changing of the reagents must then be confirmed appropriately in the software as soon as the Reagent Tray has been put back into the chamber. Failure to do all of the above will result in a mismatch between the calculated reagents available as shown in the Reagent Control and the actual reagent amounts in the containers or space available in the waste container. The reagent control function that monitors reagent and waste levels can be turned off. See “Disabling the Reagent Control”, for more information. 50 Cedex Analyzer Operator’s Guide Preparing the Analyzer for Measurements Preparing the Reagent Kit 2.5.2. Refilling Containers Individually In order to ensure optimal functioning of the analyzer, each Reagent Kit container must be thoroughly cleaned before refilling. Impurities such as dust and fluff or contamination with micro-organisms may thus be avoided. Reagents can be refilled, or emptied in the case of waste, on an individual basis. Each change can be individually confirmed by clicking on the respective Set Full button or Empty button, in the case of waste, in the Reagent Kit Status window (see Figure 39). If you are using your own reagents, it may be necessary to filter them before use. Roche Diagnostics GmbH recommends using the Cedex Reagent Kit. To refill individual containers with reagents, follow the instructions below: 1 Rinse all reagent containers well before refilling! Ensure there are no impurities such as dust or fluff in the containers. 2 Fill the detergent container to the required level with Cedex Detergent (see label or bottom of container). Only Cedex Detergent or a detergent with identical specifications should be used for the cleaning procedures in order to prevent damage to the sensitive surface of the Liquid Management components. 3 Fill Roche Diagnostics GmbH Cleaning Solution in the cleaning solution container to the required level (see label or bottom of container). 4 Fill distilled or de-ionized water in the water container to the required level (see label or bottom of container). 5 Fill 0.2% Trypan Blue solution in the Trypan Blue container to the required level (see label or bottom of container). Roche Diagnostics GmbH recommends using 0.2% Trypan Blue solution. If necessary, dilute a more concentrated Trypan Blue solution with buffer (Phosphate Buffered Saline (PBS), pH 7.4). 6 Place all of the reagent containers, as well as the emptied waste container, in the appropriate positions in the Reagent Tray (see Figure 38). 7 A Cedex Sample Cup should always be attached to the single sample port (see Figure 40). The Cedex Sample Cup (4 ml) is correctly attached when it is in an upright position beneath the sample port and the capillary tube almost reaches the bottom of the Cedex Sample Cup. If there is a Multi Sampler connected to the analyzer, a Cedex Sample Cup must be placed in the DefaultCup position on the Multi Sample Tray (see “The Multi Sampler”). C ■ Operation 51 Preparing the Analyzer for Measurments Checking the Analyzer 2.6 Checking the Analyzer Since measurement results obtained with the Cedex Analyzer depend on correctly filled reagent containers and the proper performance of the analyzer, the user should check the analyzer for possible wear and tear, and also check whether the reagent containers have the correct volume prior to each set of measurements, as follows: C 52 1 Check the syringe module (2.5 ml syringe and 8-way valve) for wear and tear or contamination. Renew the syringe if required (see “Syringe Maintenance”). 2 Check the number of runs possible. This is listed in the right-hand corner of the Control Center next to a green or red circle. Change the Reagent Kit punctually. Observe the reminder to change the Reagent Kit (see “Installing or Changing the Reagent Kit“). 3 Check whether there is an empty Cedex Sample Cup attached to the sample port or a Cedex Sample Cup in the DefaultCup position on the sample tray in the case of a Multi Sampler. If there isn’t, attach one (see Figure 40 or “Working with the Multi Sampler“). 4 Perform a Hardware Management (HW) Startup if necessary. 5 Perform a Prime if a Reagent Kit is installed and new measurements are to be carried out (see “Performing a HW Startup and Prime”). 6 Have the cell suspension samples or particle solutions ready for the analysis. ■ Cedex Analyzer Operator’s Guide Carrying out a Single Measurement 3 Carrying out a Single Measurement The following section describes the procedure for carrying out a single measurement. For setting up and carrying out multiple measurements, see “Working with the Multi Sampler”. A number of relevant parameters and entries must be specified in the Measurement window prior to carrying out measurements. They include: Choosing the operating mode and specifying sample data. Defining the measurement and analysis (process) parameters. The measurement procedure can only begin when the steps above have been completed. Perform a HW Startup and Prime prior to the first measurement if the Liquid and Hardware Management system were previously shut down (see “Performing a HW Startup and Prime”). Operation C 53 Carrying out a Single Measurement Opening the Measurement window and specifying the Operating Mode and Sample Data 3.1 Opening the Measurement window and specifying the Operating Mode and Sample Data Open the Measurement window either by clicking on the Measure button in the Shortcuts area or by selecting Single Measurement in the Measurements menu. The entry areas for choosing the desired operation and specifying the sample data are located in the Sample Parameters and Processing parameters areas of the Measurement window. The parameters should be entered just before measuring in order to ensure a direct relationship between the sample and the data. Follow the instructions below to specify sample data for a single measurement: C 1 Open the Measurement window by clicking on the Measure button in the Shortcuts area or by selecting Single Measurement in the Measurements menu. 2 Enter a clearly defined Reactor ID to describe the sample (e.g., the name of the cell culture) in the Reactor ID area. You may either choose a Reactor ID from the drop down list or enter a new Reactor ID. A new entry can be defined by up to 20 alphanumerical symbols. 3 Enter a clearly defined Sample ID in the Sample ID area (e.g., P001). The Sample ID can be freely defined. If the intended measurement is not the first in a row of measurements, i.e., if it has the same Reactor ID as a previous measurement, then the software will automatically enter the consecutive Sample ID into the Sample ID area (e.g., P001, P002,...). In that case, it is not necessary to enter the Sample ID manually unless a different Sample ID is desired. 4 If desired, use the Sample Drawing drop-down menu to select the date when the sample was drawn. Note that the process date and time, i.e., the date and time the sample was measured, is automatically entered. 5 Choose the appropriate dilution factor from the Dilution drop-down list (e.g., 1:1, 1:2, 1:5… etc.). When a dilution of 1:2 is prepared, then 1 part cell suspension has been added to 1 part dilution medium. A dilution of 1:5 means that 1 part cell suspension has been added to 4 parts dilution medium. For undiluted samples, a dilution factor of 1:1 should be entered. It may be necessary to dilute samples with very high cell densities ( >1 × 10 7 cells/ml) manually prior to measuring. The dilution ratio chosen from the drop down list only relates to the manual dilution of the sample prior to placing the sample on the system. Dilutions that are an automatic part of the measurement process in the analyzer are already taken into account by the Cedex Analyzer software. The calculations are carried out automatically and have nothing to do with the entered dilutions. 6 Select the sample volume of 1000 µl in the Volume drop-down menu. Currently, only the 1000 µl option is available for the Cedex Analyzer. 7 The System name, as well as the process date and time of the assignment, will be automatically transferred to the “Processing parameters” area in the Measurement window. 8 Entering a comment for a measurement is optional. Enter the remarks in the Comment box on the Sample Identification parameters area, if desired. ■ 54 Cedex Analyzer Operator’s Guide Carrying out a Single Measurement Defining the Measurement and Analysis (Process) Parameters 3.2 Defining the Measurement and Analysis (Process) Parameters The measurement and analysis parameters are defined in the Processing Parameters area of the Measurement window. In principle, all routine measurements can be carried out using the standardized default settings that are factory set. To change the settings, follow the instructions below: 1 Select the sample port type in the Sample Port drop-down list: Auto: this option will only appear on systems with Multi Samplers. Single: this option will only appear on systems with a single sample port. 2 Manually enter the cup position for the sample in the Cup Position window if there is a Multi Sampler (see “Working with the Multi Sampler”). In the case of single measurements run via the Measurement window on a Cedex Analyzer with a Multi Sampler attached, the software will automatically incrementally increase the sample cup position number with each new measurement. The cup position can also be fixed (see “Turning off automatic incrementation of sample cup position”). 3 Select the Cell Type that optimally recognizes your cells from the Cell Type drop-down list (see “Adjustment of the Image Analysis using the Live Operator”). The following Cell Type is available by default: Std. Cells (V5.00) for normal sized cells with a diameter of about 12 µm, e.g., HB58 If a new Cell Type has been created, it can also be selected from the same Cell Type drop-down list. See “Adjustment of the Image Analysis using the Live Operator” for more detailed information about creating new Cell Types. 4 C Select the desired precision level in the Precision drop-down list. The precision level determines the volume to be analyzed. A higher analyzed volume will require a somewhat longer measurement time but more cells will be counted, which will lead to a more precise calculation. Minimum: approximately 10 images are used for the analysis. Normal: approximately 20 images are used for the analysis. Superior: approximately 30 images are used for the analysis. The precision names may appear differently if the system has been upgraded from some previous version to software version 2.2. In the case of a system that has been upgraded to version 2.2, the precision levels may be called Low (corresponding to Minimum), Medium (corresponding to Normal) and High (corresponding to Superior). The same volumes are analyzed for the corresponding levels. 5 Prepare the sample and attach the Cedex Sample Cup containing the sample to the sample port or place it in the appropriate spot on the Multi Sample Tray (see “Preparing the Sample and Attaching it to the Multi Sample Tray or Sample Port”, below). ■ Operation 55 Carrying out a Single Measurement Preparing the Sample and Attaching it to the Multi Sample Tray or Sample Port 3.3 Preparing the Sample and Attaching it to the Multi Sample Tray or Sample Port Prepare the sample prior to measuring according to the following instructions: 1 Transfer the selected volume of a well-mixed cell suspension to a clean Cedex Sample Cup. The Cedex Analyzer tolerates volume variations of +/- 10%. Any greater variation in sample volume will lead to inaccurate results, and the Reagent Control monitor will no longer function correctly. The Cedex Analyzer can determine cell concentrations in the range of between 5 × 10 4 – 1× 10 7 cells /ml. Any higher concentration requires a manual dilution. Cells with a diameter range of between 8 µm – 40 µm can be assessed accurately. 2 Remove the present Cedex Sample Cup from the sample port (or Multi Sample Tray). 3 Attach the prepared Cedex Sample Cup containing the cell suspension to the sample port (see Figure 40; the Cedex Sample Cup is correctly attached to the sample port when it is in an upright position directly beneath it and the capillary tube almost reaches the base of the Cedex Sample Cup) or place in the appropriate cup position on the Multi Sample Tray (see Figure 42). C Figure 40: Attaching the Cedex Sample Cup to the sample port ■ 3.3.1. Starting the Measurement First ensure that the entire measurement system, including the sample, is ready for a measurement as follows: 1 Ensure that the Cedex Sample Cup is correctly attached to the sample port or placed on the Multi Sample tray. 2 Ensure that the reagent containers are sufficiently filled and in their correct positions. 3 Ensure that the waste container is empty. 4 Click on Start Measurement in the middle of the Measurement window to begin the measurement. ■ During the measurement, samples of the cell/trypan blue mixture are injected into the flow chamber in successive steps. After each injection, an image of the sample is taken and sent to the computer for analysis. The number of images taken depends on the precision level determined for the measurement. 56 Cedex Analyzer Operator’s Guide Carrying out a Single Measurement Preparing the Sample and Attaching it to the Multi Sample Tray or Sample Port 3.3.2. End of Measurement A cleaning procedure automatically begins immediately after the last image is captured and the results have been displayed in the Measurement window. The entire Liquid Management system is rinsed during this procedure (Ultra Fast Clean). Once this procedure has been completed, a green bar appears in the Measurement window. In addition, the message “Process finished EndEvent (Measurement)” appears in the Event window on the Cedex Control Center. In the Measurement window, the top section of the Result Data area displays the overall results of the measurement. The bottom section displays, in succession, the results from each image taken. When a line is selected in the list of results of single images, the corresponding image will be displayed in the Image area (see “Image Area”). C Figure 41: Cedex Analyzer Measurement window with the final results The measurement results can be directly printed out via the Print button in the middle of the measurement window. To set up a new measurement, click on the New Measurement button in the middle of the Measurement window. If the next measurement belongs to the same Reactor ID as previous measurements, then the consecutive Sample ID will automatically be entered into the Sample ID area by the analysis software without further entries being necessary. If a different Sample ID is desired, the new Sample ID can be typed in manually. Operation 57 Carrying out a Single Measurement Interrupting a Measurement When the final measurement in a set of samples has been completed, or if there is a longer pause before the next measurement, the user should carry out a Standard Clean in the Liquid Management system in addition to the Ultra Fast Clean procedure that is automatically carried out between measurements (see “Cleaning Options”). If multiple users have been created for the Cedex Software 2.2, log out of the software once the cleaning procedure has been completed to allow the next user access to the Cedex Analyzer. The Cedex Sample Cup from the last measurement should remain attached to the sample port or left in the Multi Sampler Tray in the DefaultCup position during the complete cleaning procedure. The cup should only be removed when a new Cedex Sample Cup has been attached for the next measurement. C If the Cedex Analyzer is to be shut down after a set of measurements, or at the end of the day, the complete Liquid Management system should be cleaned with an LM Shutdown procedure to maximize the life-span of the Cedex Analyzer and guarantee optimal performance. The entire Liquid Management system is rinsed with distilled or de-ionized water during the LM Shutdown, and the Trypan Blue is then pumped out of the capillary (see “Carrying out an LM Shutdown and HW Shutdown”). 3.4 Interrupting a Measurement An orange EMERGENCY STOP button is located on the left-hand side of the Measurement window and can be activated during the measuring procedure to interrupt the analysis process. If the EMERGENCY STOP is selected, an error message will appear asking, “Do you want to cancel the process?”. Click on Yes to stop to stop and abort the process immediately. Click on No to put the process on hold. If Yes is selected, the EMERGENCY STOP button will change to read Unlock Queue. The system must be unlocked by clicking on this button before more measurements can be run. If No is selected, the EMERGENCY STOP button will change to read Resume. Click on this button to resume the measurement process. Only use the Emergency Stop button in a case of emergency. Actual measurement data may be lost. 58 Cedex Analyzer Operator’s Guide Working with the Multi Sampler 4 Working with the Multi Sampler Moving parts of the Multi Sampler may cause hand injuries. The Multi Sampler needle may cause injuries during operation. Never use the Cedex Analyzer without the protective cover in place for the Multi Sampler. The Multi Sampler is an accessory device for the Cedex Analyzer (see Figure 42 and Figure 43). The Multi Sampler can convey up to 20 cell suspension samples in sequence to the Cedex System for analysis. Once the samples have been loaded in the Multi Sample Tray and the analysis parameters for each sample have been set, the samples are automatically delivered to the Cedex System and analyzed. C Protective Cover Sampling probe Cedex Sample Cups Multi Sample Tray Figure 42: Multi Sampler Operation 59 Working with the Multi Sampler The Multi Sampler DefaultCup C Sampling probe Multi Sample Tray Figure 43: Cedex Analyzer including Multi Sampler 4.1 The Multi Sampler DefaultCup The position of the Cedex Sample Cup used for the Prime, LM Shutdown, calibration and cleaning routines is called the DefaultCup. This sample cup does not differ from the usual Cedex Sample Cups. The standard (default) position for the DefaultCup is position 1 of the Multi Sample Tray. The 20 numbered positions are clearly marked directly on the Multi Sample Tray. An empty Cedex Sample Cup must be manually placed in the position set for the DefaultCup before running LM Shutdown, focus adjustment, Prime and all cleaning routines. The position in which the DefaultCup is placed can be changed. See “Modifying the Standard Setting for the Multi Sampler DefaultCup”). The position of the DefaultCup does not influence measurements. All 20 positions on the Multi Sample Tray can be used for measurements. However, should a sample be present in the DefaultCup position during Prime, LM Shutdown, focus adjustment or any cleaning routines, it can no longer be used for a measurement. 60 Cedex Analyzer Operator’s Guide Working with the Multi Sampler Preparing the Measurement 4.2 Preparing the Measurement 4.2.1. Using the Multi Sample Tray Fill the appropriate volume of samples into Cedex Sample Cups (maximum 20) and place them on the Multi Sample Tray according to the desired sequence. Gently insert the tray into the notch until the automatic tray rope starts pulling it in. As a safety precaution, leave all of the empty Cedex Sample Cups in the Multi Sample Tray after the measurements have been completed. 4.2.2. Ejecting the Multi Sample Tray The Multi Sample Tray can be ejected by gently pushing on the tray only when the system is idle. The tray cannot be ejected if the system is moving or the needle is down in a cup. If a problem occurs with the system when the needle is down (see, for example, “Disruption of Measurements”), restart the Hardware Management to render the tray ejectable again (see “Carrying out an LM Shutdown and HW Shutdown”). In some cases it may be necessary to restart the Cedex Software 2.2 and Analyzer. 4.2.3. C Performing a Prime The Prime and HW Startup are performed as usual in the Liquid Management window as described in “Performing a HW Startup and Prime”. An empty Cedex Sample Cup must be placed in the DefaultCup position (default position 1) of the Multi Sample Tray when running a Prime. 4.3 Carrying out Measurements with the Multi Sampler Before carrying out measurements, ensure that the system is operational as described in “Checking the Analyzer”. 4.3.1. The Multi Run Data Entry Window Click on the Multi Run button in the Shortcuts area of the Cedex Control Center or select Multi Run in the Measurements menu. The Multi Run window will appear, and entries for sample data and parameters for the analysis process are entered via this window (see Figure 44). In addition to the entry columns for ReactorID, SampleID, Cell Type, Dilution and Precision (see “Opening the Measurement window and specifying the Operating Mode and Sample Data” for more details), there are also columns for Status and CupNr. The CupNr column shows the sample cup position on the Multi Sample Tray. The Status column displays the state of the sample before, during and at the end of a measurement. Operation 61 Working with the Multi Sampler Carrying out Measurements with the Multi Sampler 4.3.2. Preparing for Multiple Measurements in the Multi Run Window The Multi Run window automatically displays all 20 possible sample cup positions. To set up and carry out multiple measurements with the Multi Run do the following: C 1 Transfer 1000 µl of a cell suspension sample into Cedex Sample Cups and place the cups in the desired locations on the Multi Sample Tray. 2 Click anywhere in the row of the MultiRun Measurements Preparation area that corresponds to the location of a Cedex Sample Cup containing a sample. The row will be converted to edit mode, and the sample and process parameters for the measurement can be defined (see “Opening the Measurement window and specifying the Operating Mode and Sample Data” and Figure 44). 3 Enter the desired sample data and parameters for the sample (see “Defining the Measurement and Analysis (Process) Parameters”). 4 Enter a comment in the field Comment, if desired. 5 Repeat steps 2 – 4 for the remaining samples to be measured. 6 The rows in which entries are in the process of being filled out will remain in edit mode. To clear the entire list of entries and start with a new list, click on the Clear List button on the right-hand side of the Multi Run window. ■ Measurement of up to 20 samples in a row leads to prolonged incubation (up to 90 minutes) of cells at room temperature. Tests in our lab using several different cell lines (CHO-K1 and several hybridoma cell lines) showed no noteworthy influence of the prolonged incubation times on the measurement results. However, this result may not necessarily apply to all cell lines available on the market. We, therefore, recommend testing especially sensitive cell lines in advance to determine the number of samples that can be measured in a row without affecting the cells. Figure 44: Adding sample information to the Multi Run window 62 Cedex Analyzer Operator’s Guide Working with the Multi Sampler Carrying out Measurements with the Multi Sampler 4.3.3. Activating Sample Rows and Starting the Measurement After all sample information has been entered in the Multi Run preparation area, the samples can be activated and, thus, added to the process queue. To activate samples and start the measurement, do the following: 1 Activate the status of each sample row by double clicking in the Status field of the row to be activated. The row appears pale blue, and further modifications of sample information is impossible. Return to the Edit status by double clicking on the Status area of the sample row to allow for further changes, if required. 2 Alternatively, all samples can be activated or deactivated simultaneously by double clicking on the word Status in the column heading at the top of the Multi Run preparation area. Confirm the safety query with Yes to accept the modification. 3 After some or all rows have been activated, click on the Start button on the right-hand side of the Multi Run window to start the analysis of the activated measurements. ■ When measuring begins, the row of the sample being measured will be highlighted in yellow, and the progress of the measurement will be tracked in the status column. When a measurement is finished, the row will be highlighted in green and status column will indicate Done. In addition, the estimated time required for the measurement is shown in the Estimated time remaining field. Images taken of the sample are displayed in the upper right-hand corner of the Multi Run window during the measurement. In addition, results for Total Cell Concentration, Viable Cell Concentration and Viability are displayed in the upper left-hand corner of the Multi Run window during and after a measurement has finished. C Before, during and after measuring, the Status column can display the following information (see Figure 44, above and Figure 45): Edit: Indicates that sample data is actively open for editing and is in the process of being edited. Sample data in edit mode has not yet been added to the process queue, and samples placed in positions in edit mode will not be analyzed when the Multi Run is started. Rows in edit mode are white. Active: Indicates that the sample is ready for analysis, which starts automatically once the Start button is pressed. Rows in active mode are highlighted light blue. Scheduled: All rows marked as active will be added to the process queue and converted to scheduled mode after pressing the Start button. Rows marked as edit will remain in edit mode. Prepare: Indicates that the system is preparing to measure the sample marked with this status. The row is highlighted in yellow. Measure: Indicates that the system is in the middle of carrying out a measurement of the sample marked with this status. The row is highlighted in yellow. Cleaning: Indicates that the system is carrying out the cleaning routine after a completion of a measurement. The row is highlighted in yellow. Done: indicates that measurement and analysis of a sample marked with this status has been completed successfully. The row is highlighted in green. Failed: The measurement of this cup has failed. Aborted: The measurement of this cup has been aborted by the user. No Cup: There was no cup at this position in the multi sampler when it was ready for measurement. Blocked: The lift was blocked when the cup should have been measured. The status of a particular measurement is tracked in the Status column. The Errors and messages window gives a list of each step completed and any errors that may have occurred. Operation 63 Working with the Multi Sampler Carrying out Measurements with the Multi Sampler C Figure 45: Multi Run window during measurement Only samples that have the status of active or scheduled will be measured. Samples that are in edit mode have not yet been added to the process queue and will not be measured until they have been activated. If an automated cleaning has been scheduled via the Scheduler function, the cleaning routine has a lower priority than scheduled measurements and will be added to the process queue after all activated (status: active or scheduled) measurements have been carried out (see “Scheduling Automatic Cleaning Routines” for more information about automating cleaning routines). Note that measurement information placed in the Multi Run preparation area that have the status of edit are not added to the queue! Therefore, if a Cedex Sample Cup containing a sample is added to the Multi Sample Tray in the DefaultCup position, and the row for that sample is left in edit mode, the cup will be used for a cleaning routine should one be scheduled to be carried out at that time. It is therefore critical to ensure that a Cedex Sample Cup containing a sample to be measured is never placed in the DefaultCup position on Multi Sample tray and left in edit mode during a Multi Run. Samples placed in the DefaultCup position for measurement should be immediately set to active or scheduled in order to be added to the process queue and, thus, have precedence over all scheduled cleaning routines. 4.3.4. Adding Measurements to the List while Measurements are Running Sample rows in which data has not yet been entered can be filled out at any time while the Multi Run is running. In addition, sample rows containing finished measurements (status: done) can be cleared and prepared for a new measurement by double-clicking in the Status field of the row with the finished measurement. Sample data for a measurement cannot be modified after that measurement has begun. 64 Cedex Analyzer Operator’s Guide Working with the Multi Sampler Interrupting a Multi Run 4.3.5. Modifying Data Entry, Changing Samples Information about the operation and process parameters for samples that have not yet been analyzed can be modified during the run. To modify information of measurements that are in active or schedule mode but have not yet been started, do the following: 1 Double-click on the Status field of the measurement to be modified. The status field will indicate that the sample is in edit mode. 2 Make desired changes to the measurement. 3 Double-click on the Status field to re-activate the measurement (status: active or scheduled). ■ Wait until the Multi Sample Tray has stopped moving before changing the samples! 4.3.6. Non-Linear Measurements in a Sample Series Measurements of activated samples are always done in a linear fashion following a sequence of 1 – 20. If samples need to be analyzed individually and not in the usual linear ascending order of 1 – 20, the samples to be analyzed later should be inactivated and remain in the Edit status for the meantime. When all active samples in the sample tray are completed, subsequent measurements with the newly activated samples can begin. 4.4 C Interrupting a Multi Run The Start button will switch to a Stop button after a Multi Run has started. Click on the Stop button to pause or stop the Multi Run. If a measurement is being carried out when the Stop button is pressed, that measurement will be completed. All scheduled measurements (status: scheduled) will switch to active mode, and the Stop button will revert to Start. Click on the Start button again to continue analysis of activated measurements. 4.5 Disruption of Measurements Error messages may appear if a sample can’t be run. For example: If a Cedex Sample Cup is not available in its position on the Multi Sample Tray during measurements, then the No Cup message will appear. If the Multi Sample Tray is not inserted or not inserted correctly, then the Tray not inserted message will appear. Some errors may block the analysis of the rest of the measurements. The level of error that should stop the analysis of all samples can be determined using the Error Level drop-down list at the top of the Multi Run window. The options for the level of error that will stop the analysis are: Fatal: Only errors involving a system / hardware crash, when functionality is not available, will stop analysis. Critical: Data loss or any other error that results in an invalid measurement will stop the analysis. Error: Errors that do not result in an invalid measurement will stop the analysis. Warning: Warning messages with information for the user will stop the analysis. Message: Any message will stop the analysis. Operation 65 Working with the Multi Sampler Results 4.6 Results After a Multi Run has finished, the results for all measurements obtained by the Cedex Analyzer are stored and displayed as described in chapter 7 “Using the Measurement List”. In addition, some results for the measurements carried out are displayed in the Analyzed Measurements field at the bottom of the Multi Run window. 4.6.1. The Multi Run Result List At the bottom of the Multi Run window, the Analyzed Measurements field displays the list of results for measurements previously carried out. Measurements are listed in order of process time, from the newest measurements at the top of the list to the oldest measurements at the bottom. All measurements carried out using the Multi Run window will be displayed in this field unless the Clear Resultlist button has been pressed. C Clicking on the Clear Resultlist button will clear all measurement results from the list. In addition, measurements displayed in this field can be restricted to only the measurements carried out by the user logged into the system (mine), measurements that have not yet been printed out (unprinted), and/or measurements carried out on that particular day (today). Measurement results can be printed out via the Print Report button located just above the Analyzed Measurements field (see “Printing Reports” for more information about print report options). The following information is shown in the result list: User Workarea Reactor ID (classifying the cell sample) Sample ID (naming the measurement) Valid check-box Total cell concentration [× 105 cells/ml] Viable cell concentration [× 105 cells/ml] Viability [%] Sample Drawing (defined by user, if desired) Process Time (date and time sample was measured) Comment (if added by the user) Other results, such as Average Diameter, can be added for display in the result list via the User Preferences (see “Adjusting Result Display in the Measurement List and Multi Run windows”). Double-click on a measurement to view all results. If the result list has been cleared, previously carried out measurements can still be viewed, printed out and exported via the Measurement List window (see “Using the Measurement List”). 66 Cedex Analyzer Operator’s Guide Switching off the Cedex Analyzer Carrying out an LM Shutdown and HW Shutdown 5 Switching off the Cedex Analyzer Switching off the Cedex Analyzer should always be carried out in the following order: 1 Carry out an LM Shutdown. 2 Shut down the analysis software (optional, see note below regarding the use of the scheduler). 3 Shut down the operating system. 4 Switch off the individual devices at random. ■ If Prime, LM Shutdown or routine cleaning routines have been scheduled via the scheduler, the software application must be left on and the HW must be started (see “Scheduling Automatic Cleaning Routines”). 5.1 Carrying out an LM Shutdown and HW Shutdown C All of the capillary tubes in the Liquid Management system are cleaned and rinsed with distilled or de-ionized water during an LM Shutdown. In addition, the Trypan Blue is withdrawn from the 8-way valve/syringe and replaced with air. This is to prevent the capillary tubes and flow chamber from becoming damaged. The HW Shutdown shuts down several elements of the hardware system including the Multi Sampler (if present) and pump. Follow the instructions below to carry out an LM Shutdown: 1 Click on the HWM button in the Shortcuts area of the Control Center to open the Hardware Management window. Alternatively, the Hardware Management window can be opened by selecting Hardware Management in the Functions menu at the top of the Control Center (see Figure 46). 2 Click on the LM Shutdown button in the lower right-hand corner of the window to shut down the Liquid Management. The estimated time required for the LM Shutdown is displayed in the “Estimated Total Time” section of the Hardware Management window. 3 When everything has been shut down, the Current Status field will have the message “HW started and LM not primed”. If both the Liquid Management and the Hardware Management has been shut down, the the message “HW not started and LM not primed” will appear. 4 Click on to close the window. ■ Figure 46: Hardware management window See also “The Hardware Management Window”. Operation 67 Switching off the Cedex Analyzer Logging out 5.2 Logging out To log out of the Cedex Control Center, select Logout under the System menu or click on the Logout button in the Cedex Control Center. If an LM Shutdown has not yet been carried out, the message, “Do you really want to log out without performing an LM Shutdown?”, will appear. Either click on Yes to log out immediately or click on No, perform an LM Shutdown, then log out. The software will be ended and the login window will reappear. Logout is possible during a measurement without influencing it. A message indicates that measurements are in progress. C 5.3 Shutting down the Control Center Follow the instructions below: 1 Perform an LM Shutdown to shut down the Liquid Management system (see “Carrying out an LM Shutdown”). 2 Shut down the software by selecting Exit under the System menu or by clicking on to close the window. The security query, “Do you really want to exit the Cedex Control Center?“, will appear. 3 Click on Yes to shut down the program. ■ Restarting the analysis software is necessary for the next measurement session(see “Starting the Cedex Software 2.2”). If at all possible, the analyzer should never be turned off. If it is necessary to turn it off, the analyzer needs at least 2 hours to warm up before it can be used for measurements. 68 Cedex Analyzer Operator’s Guide Using the Measurement Results Window D Software 1 Using the Measurement Results Window Measurement results are displayed in the Measurement window (see Figure 48). If a single measurement has been run using the Measurement window, the analysis results obtained from that measurement are automatically displayed in the same window after the analysis process has been completed. Measurement results from Multi Runs are displayed in the Multi Run result list until the list has been cleared. In addition, measurement results can be viewed via the Measurement List window. To access this window, click on the List button in the Shortcuts area of the Cedex Control Center or select Measurement List in the Measurements menu. The Measurement List window will open, showing all of the measurements stored in the database (see Figure 47). See “Using the Measurement List” for more details about working with the Measurement List. D Figure 47: Measurement List window To see the results of a particular measurement, highlight the row containing the measurement to be viewed by clicking on the field to the left of the appropriate line, then clicking on the View button in the bottom right-hand corner. The Measurement window will open with the results of that particular measurement. The Measurement window has 4 separate sections (see Figure 48): Result Data area Sample Parameters area Processing Parameters area Image area Some of the obtained data can also be displayed as graphic diagrams by clicking on the Diagrams button (see “Graphical Display of the Analysis Results” and “Cultivation Time Chart” for more details). It is also possible to access the Live Operator from this window by clicking on the Live Operator button (see “Adjustment of the Image Analysis using the Live Operator”). Software 69 Using the Measurement Results Window Result Data area 1.1 Result Data area The Result Data area in the bottom half of the Measurement window has two separate sections: the section just below the words “Result Data” displays the overall results for the measurement, while the section further down displays the results for each image analyzed. D Figure 48: The Measurement window with results The parameters shown in the Result Data area for both the overall results and individual image results include: Viable Cell Conc. Value: This value indicates the concentration of viable cells [×105 cells/ml]. Total Cell Conc. Value: This value indicates the total cell concentration [×105 cells/ml]. Viability (%) Value: This value indicates the proportion of viable cells (%) to the total number of cells (viable and dead cells). Avg Compactness Value: This value indicates the average variation, in shape, of viable cells from an ideal sphere, with the ideal sphere shape equaling >1<. Higher values indicate the extent of variation and, therefore, the overall state of the cell culture (e.g., damage caused by shear force etc.). Average Diameter Value: This value indicates the average diameter of viable cells [µm]. Aggregate Rate Value: The Aggregate Rate specifies the percentage of all cells (Total Cell Count) present in aggregates (clusters). Dead Cell Conc. Value: This value indicates the dead cell concentration [×105 cells/ml]. Viable Cell Count Value: This value indicates the number of viable cells counted. Dead Cell Count Value: This value indicates the number of dead cells counted. Total Object Count Value: This value indicates the total number of all detected objects counted. 70 Cedex Analyzer Operator’s Guide Using the Measurement Results Window Sample Parameters and Processing Parameters areas In addition, the Result Data area for the individual images has an Excluded column next to the image number. Images that could lead to incorrect measurement results during analysis, e.g., due to impurities or large bubbles, are automatically recognized as invalid and excluded from evaluation by the analysis software. If this occurs, the image will be marked with a check in the checkbox of the Excluded column. Users can also manually exclude individual images from the calculations or include images that were automatically excluded by the software by clicking on the check-box in this column. 1.2 Sample Parameters and Processing Parameters areas The Sample Parameters area of the Measurement window shows the parameters entered by the user before running the measurement. If any measurements have been reprocessed, the original or reprocessed data can be selected in the drop-down menu of the Data Set section. If data has been reprocessed at some point, the Effective checkbox will indicate which data set has been determined to be the effective version (see “The Reprocess Button”). Comments for the measurement can be added in this area at any time. The Processing Parameters area lists the process parameters of the measurement, including Cell Type, used to analyze the images (see “Adjustment of the Image Analysis using the Live Operator”), the precision selected and the date and time the process was run. None of the values in this area can be changed. Click on the Show parameters button below the Cell Type drop-down menu to open a window that shows the actual Live Operator Parameters values used for that Cell Type (see Figure 49, below). D Figure 49: Window displaying the Live Operator parameter settings for the Cell Type used for a measurement Software 71 Using the Measurement Results Window Image Area 1.3 Image Area 1.3.1. Viewing Individual Cell Images The Cedex Software 2.2 enables a close view of a single image or an enlarged display for evaluation. Individual images can be viewed in the Image area of the Measurement window. The results from the individual images are listed at the bottom of the Measurement window in the Result Data area. When a row with the results of a particular image is highlighted in this section, the image connected with those results is displayed in the Image area at the top right-hand corner of the Measurement window. To see a different image in this area, click on a different row in the Result Data area. Only one image is displayed in the Image area in the Measurement window. Alternatively, an overview of all cell images can be displayed by clicking on the Image List button beneath the Image area, which will display the Image List window containing thumbnails of all of the images used for the calculation of results (see Figure 50, below). D Figure 50: Image List window showing all images used for the analysis Double-click on an image in the Image List window to open a new window, called the Image View. This window contains an enlarged version of the selected image, as well as some further options for viewing the image. Double-clicking on the image displayed in the Image area of the Measurement window will also open the Image View window. The image list also displays an image taken of the analyzed area in the flow chamber just before cells are introduced into the chamber (Prescan Image). This image can be used to check whether large impurities that might affect the image analysis are present in the analyzed area of the flow chamber. 72 Cedex Analyzer Operator’s Guide Using the Measurement Results Window Image Area 1.3.2. Viewing a Cell Image Using the Image View Window It is possible to see which cells were marked viable and dead cells by the analysis software via the Image View window. The user can thus get a sense of how cell shapes and clusters have been evaluated by the software. The Cedex Software 2.2 offers various options for optimizing measurement results by adjusting the Operator used for the analysis. Thus, the image analysis Operator can be adjusted for abnormal cell culture images or for specific internal counting strategies. For more information about adjusting the image analysis, see “Adjustment of the Image Analysis using the Live Operator”. The Image View offers the following information and options: Viable Cells: number of viable cells. Dead Cells: number of dead cells. Show Circles check-box: switches on/off the marking of cells recognized as living or dead. Viable cells are marked with a uniform green circle and dead cells are marked with a red circle. The circle diameter corresponds to the cell diameter. Objects are marked with a blue circle. Zoom: Image enlargement. Brightness and contrast settings. Navigating a window when the image is enlarged (scroll bars appear at the bottom and right edge of the image when the image is zoomed in). Scrolling through all of the images for a particular measurement using the arrows lower right-hand corner. in the D Figure 51: Viewing a cell image using the Image View window Software 73 Using the Measurement Results Window Image Area Certain areas of the image can be enlarged by following the instructions below: 1 Place the mouse pointer on the top left-hand corner of the area to be enlarged. 2 Hold the left mouse button pressed down and move it to the lower right-hand corner of the area to be enlarged. 3 Release the mouse button; the selected area will fill the whole window. ■ Return to the original size of the image by following the instructions below: 1 Place the mouse pointer anywhere on the diagram. 2 Hold the left mouse button pressed down and form a box from the bottom right corner to the upper left corner. 3 Release the mouse button. The chart will then return to in its original size. ■ Click on Close to shut the window or use the D 1.3.3. button. Excluding Images from the Evaluation Process/Including Excluded Images Images can be excluded from analysis by the user. Also, images that have been excluded automatically by the analysis software (due to, for example, excessive bubbles or dirt) can be included in the result analysis, if desired. Exclusion and inclusion of images for a particular measurement are done via the check-box in the Excluded column in the Result Data area of the Measurement window. If there is a check in the Valid check-box, the image is considered valid, which means that the cell image has been included in the calculation process. The user can choose to manually exclude the image by clicking on the checkbox in the Excluded column for the selected image. The image will still be marked as Valid, but will also be excluded from the calculation of results. No check in the Valid check box means that the cell image is not considered valid and has been automatically excluded from the calculation process. In that case, a check-mark will automatically appear in the Excluded column. To include an image that was excluded by the software, click away the check-mark in the Excluded column. The image will still be marked as invalid via the lack of check-mark in the Valid check-box, but will be included in the calculation of results. 74 Cedex Analyzer Operator’s Guide Using the Measurement List 2 Using the Measurement List Data from measurements that have been carried out and stored in the database can be accessed via the Measurement List window. Open the Measurement List window by either clicking on the List button in the Shortcuts area of the Cedex Control Center or by selecting Measurement List in the Measurements menu at the top of the Control Center. Measurements are stored in the order in which they were carried out, with the most recent measurement placed at the top of the list. Two types of information can be displayed in the list of measurements: information about sample and process parameters and information about some results. If there is no check in the Show measurement results box at the bottom left-hand corner of the window, sample and process parameters for measurements are displayed (see Figure 52, below). D Figure 52: Measurement List window displaying the Sample Identification and Process Parameters To see measurement results, click on the check box next to Show measurement results (see Figure 53). By default, the list displays the results for total cell concentration, viable cell concentration and viability. Other results, such as Average Diameter or Compactness, can be added for display in the result list of the Measurement List window via the User Preferences (see “Adjusting Result Display in the Measurement List and Multi Run windows”). Figure 53: Measurement List window with the option Show measurement results selected Software 75 Using the Measurement List Viewing Existing Analysis Results A number of actions can be carried out in the Measurements List window including searching for measurements using a variety of filters, viewing measurement sample and process parameters, viewing measurement results, printing reports, exporting measurements to a file and reprocessing measurements (see “The Reprocess Button”). 2.1 Viewing Existing Analysis Results View existing data sets by double-clicking on the measurement or by highlighting the row containing the desired measurement and then clicking on the View button in the bottom right-hand corner of the Measurement List window. This will open a Measurement window containing all of the relevant data results for the selected measurement (see “Using the Measurement Results Window”). 2.2 Searching for Measurements It is possible to search for measurements using a number of different filter criteria including sample drawing date, process date, Reactor ID, and Sample ID in the Filter By area at the top of the Measurement List window. To search for measurements based on the sample drawing date or the process date, for example, do the following: D 1 Click on the drop-down menu button next to the Sample Drawing Date From or Process Date From sections. A calendar will appear in which the desired starting date for filtering can be selected. 2 When a date has been selected, a check will appear in the check-box next to the date to indicate that a filter is active based on that date. 3 Click on the drop-down menu button next to the date in order to select the desired ending date. 4 Once the dates for filtering the measurements have been selected, click on the Find button in the upper right-hand corner of the Measurement List window. 5 All of the measurements that match the dates given for sample drawing (using the Sample Drawing Date From section,) or that were run within the dates specified in the Process Date From section, will be displayed in the measurement list in the bottom half of the window. ■ It is possible to select measurements with regard to both sample drawing date and process date. If the desired dates for both the sample drawing dates and process dates are selected, only those measurements that meet all 4 date criteria will be displayed when the Find button is clicked on. Measurements can also be searched for based on Reactor ID and/or Sample ID by filling in the information in these sections of the Filter By area. In addition, measurements can be searched for based on user by typing in the user name in the User section, by work area (using the drop-down menu in the Workarea section), by data set (in the DataSet area) and by Cell Type (using the drop-down menu in the Cell Type section). If a measurement has been reprocessed, the original and all reprocessed versions of the measurement will be listed. The data set version of a particular measurement that has been selected as the Effective data set will have a check in the check-box of the DSEffective column. The original data set of a particular measurement will have a check in the check in the check-box of the DSOriginal column (see “Effective Data Sets”). 76 Cedex Analyzer Operator’s Guide Editing Existing Analysis Results/Data Sets The Reprocess Button 3 Editing Existing Analysis Results/ Data Sets The Cedex Software 2.2 allows for existing measurement results or data sets to be modified and reprocessed. These changes are done on existing software data (image and analysis results) and, therefore, do not require any adjustments to the analyzer. Existing measurement results can be edited via the Reprocess button in the lower right-hand corner of the Measurement List window. 3.1 The Reprocess Button Reprocessing existing measurement results/data sets, i.e., viewing a set of image data and evaluating them with new analysis parameters, can be done in the Reprocess mode, which is only accessible to authorized system users. The reprocess mode offers the following options: Enter, modify or delete a comment. Correct the dilution (see “Defining the Measurement and Analysis (Process) Parameters”). Change the Cell Type (see “Adjustment of the Image Analysis using the Live Operator”). To reprocess a measurement, do the following: 1 Open the Measurement List window by clicking on the List button in the Shortcuts area of the Cedex Control Center or by selecting the Measurement List option in the Measurements menu of the Control Center. 2 Highlight the row of the measurement to be reprocessed and click on the Reprocess button in the lower right-hand corner. A Measurement window will open containing all of the result data for that measurement. 3 Enter a new name for the data set in the DataSet section of the Sample Parameters area. 4 Make the desired changes to the new data set. Changes can be made with regard to the comment, dilution factor and Cell Type in the appropriate sections of the Sample Parameters and Processing Parameters areas. 5 Click on the Reprocess button in the center of the Measurement window to start the reprocessing of the measurement based on the new parameters. 6 When the reprocessing is finished a window will open asking whether the new data set should be the effective data set (see “Effective Data Sets”). D ■ A new data set is available once the evaluation has been completed. All changes can be retraced by viewing previously created data sets, which are shown in the Measurement List window. The reprocessing procedure creates additional data sets. Original data is not overwritten. Software 77 Editing Existing Analysis Results/Data Sets Effective Data Sets 3.2 Effective Data Sets When measurements are reprocessed, it is possible to label one of the resultant data sets as Effective. The Effective data set is the version of the measurement (original or reprocessed) that has the correct parameters. Once a data set has been selected as Effective it will be labeled as such in the Measurement List window. It is possible to later change which data set is labeled the Effective data set by doing the following: 1 Select the data set version of the measurement to be labeled Effective in the Measurement List window. 2 Click on the Reprocess button. A Measurement window will open containing the results for that data set. 3 Click on the box to the left of the word “Effective” in the Measurement window. A check will appear in the box. 4 Close the Measurement window. 5 Click on Find in the Measurement List window to refresh the list; the newly selected data set will appear as the Effective data set. ■ D 78 Cedex Analyzer Operator’s Guide Graphical Display of the Analysis Results Enlarging the Histograms 4 Graphical Display of the Analysis Results In addition to displaying the overall analysis values, the Cedex Software 2.2 can also display graphic diagrams of the results. These diagrams can be viewed after the analysis is finished by clicking on the Diagrams button in the Result Data area of the Measurement window. When the Diagrams button has been selected, the Diagram window will open. 4 different histograms are available: Aggregate Histogram, Cell Diameter Histogram, Compact Histogram, and Measurement Statistics. Click on the respective button to open the desired diagram. The Object Diameter Histogram function is present, but no data is delivered by the presently available Cell Type. All the results represented in the diagrams are based on valid images accepted for evaluation. This means that individual images may be sorted out due poor quality (e.g., bubbles, dirt particles, etc) in the interest of an accurate measurement result. This is done automatically by the analysis software or manually by the user (see “Excluding Images from the Evaluation Process/Including Excluded Images”). 4.1 Enlarging the Histograms Certain areas of the histograms can be enlarged by following the instructions below: 1 Place the mouse pointer on the top left-hand corner of the area to be enlarged. 2 Hold the left mouse button pressed down and move it to the lower right-hand corner of the area to be enlarged. 3 Release the mouse button and the selected area will fill the complete window. ■ D Return to the original size of the histogram by following the instructions below: 1 Place the mouse pointer anywhere on the diagram and right-click with the mouse. 2 A small window will open with the options “Unzoom” or “Undo all Zoom/Pan”. 3 If the chart was enlarged more than once, selecting “Unzoom” will reduce the image to the point before the last enlargement. Selecting “Undo all Zoom/Pan” will return the chart to its original size. ■ In addition, the diagrams can be moved around within the window by placing the mouse pointer anywhere in the diagram, holding down the middle mouse button and moving the mouse. Software 79 Graphical Display of the Analysis Results Aggregate Histogram 4.2 Aggregate Histogram The Cedex Analyzer offers an evaluation of aggregates in cell cultures. Click on the Aggregate Histogram button in the Histograms window to open the corresponding histogram window. The Aggregate Histogram shows the number of cells in the cell culture found in aggregates, as well as how many cells each aggregate is composed of. Both the actual cell number and the percentage distribution can be displayed. D Figure 54: The Aggregate Histogram, detailed view (divided into living and dead cells), here: (absolute) number of cells The Number of Cells [#] identified is displayed on the y-axis and at the top of the bars. The Aggregate Size, in terms of the number of cells per aggregate, is given on the x-axis. Figure 54 shows, for example, that 148 living and 40 dead cells of all identified cells were found in aggregates of two cells. 80 Cedex Analyzer Operator’s Guide Graphical Display of the Analysis Results Aggregate Histogram The percentages can be displayed using the percent button. Figure 55: The Aggregate Histogram, detailed view (divided into living and dead cells), here: percentage distribution of cells The percentage of cells [%] found in aggregates compared to the total live or dead cell count is displayed on the y-axis. The aggregate size, in terms of the number of cells per aggregate, is given on the x-axis. Figure 55 shows, for example, that 3.66% of all living cells and 7.29% of all dead cells are found in aggregates of two cells. The Total Cell Count (living and dead cells combined) per aggregate is mapped in the histogram using the total button. Figure 56 shows, for example, that 188 cells of the measurement are found in aggregates of two cells. D Figure 56: The Aggregate Histogram, total view (sum of living and dead cells), here: number of cells Software 81 Graphical Display of the Analysis Results Cell Diameter Histrogram The percentage of cells found in aggregates, in relation to the total cell count, can be displayed using the percent button as is shown in Figure 57. D Figure 57: The Aggregate Histogram, total view (sum of living and dead cells), Here: percentage 4.3 Cell Diameter Histogram Clicking on the Cell Diameter Histogram button will bring up the Cell Diameter Histogram. The Cell Diameter Histogram represents living cells (!) with a definable diameter. This diagram is based on the single diameters of all cells in the measurement. Figure 58: Cell Diameter Histogram 82 Cedex Analyzer Operator’s Guide Graphical Display of the Analysis Results Object Diameter Histogram 4.3.1. Defining Diameter Intervals in the Diameter Histogram The Cell Diameter Histogram has three sliders that can define separate diameter intervals. This allows for dividing a diameter histogram into a maximum of four parts. The sliders can be activated by clicking on the corresponding boxes and moving the sliders to the desired positions. One can also define the margins of the intervals by entering the numerical values on the left hand side of each slider. The borders of the first interval are defined by the minimum value and the first numerical value entered. The next two values define the upper borders of the second and third intervals. The fourth interval is defined by the upper border of the third interval and the maximum value. The number of viable cells, their percentage of the total viable cell number and the viable cell concentrations [×105 cells /ml] are listed in a table for each of the individual intervals.The intervals set in the Cell Diameter histogram can be saved for future reference. In addition, the default intervals can be automatically set for all measurements via the User Preferences (see “Specifying Default Measurement Parameters”). 4.4 Object Diameter Histogram Clicking on the Object Diameter Histogram button will bring up the Object Diameter Histogram. Analogous to the representation of the diameter of the living cells, the diameter of all recognized objects such as cells, debris, air bubbles and viable and dead cell aggregates may be displayed in this histogram depending on whether the information is provided by the image analysis software. The default image analysis software (Cell Type: Std. Size (V5.00)) delivered with the Cedex Analyzer does not provide any detailed information about objects. Therefore, clicking on the Object Diameter Histogram button will result in a message that there is nothing to display, and nothing will be shown in the diagram. Software D 83 Graphical Display of the Analysis Results Compactness Histogram 4.5 Compactness Histogram The ratio between the cell circumference and the cell area is based on an ideal sphere (4␲), which is equivalent to the value >1< on the abscissa of the Cell Compactness Histogram. The extent of variation between the cell shapes and an ideal sphere is reflected in values being greater than 1. The shape of a cell is known as the Compactness. Click on the Compactness Histogram button to display a diagram that compares viable (!) cell shapes to that of an ideal sphere. If a significant number of cells (ordinate) have a high value, this could indicate improper handling of a sample. The Compact Histogram can be used to check the state of the cell culture, e.g., if the stirring speed is too high or nutrient composition is incorrect. D Figure 59: Compactness Histogram This diagram is based on the compactness of all viable cells in the measurement. To view results of individual cell images, see “Result Data area”. 84 Cedex Analyzer Operator’s Guide Graphical Display of the Analysis Results Measurement Statistics Histogram 4.6 Measurement Statistics Histogram Click on the Measurement Statistics button to display a column diagram showing the total number of viable cells (green columns) and dead cells (red columns) found in the images analyzed. Figure 60: Measurement Statistics histogram In the bar diagram, the number of living cells is represented in green bars and the number of dead cells in red bars on top of the green bars. The Combine button, which appears when the Measurement Statistics histogram is open, can be used to combine several images to give a better overview of the whole sample. Conspicuous bars can thus be immediately identified, and the user can then view and assess the relevant images (see “Image Area”). D The results of each individual image can be seen again by clicking on the Single button. If an image has been automatically excluded by the software or manually excluded by the user, the corresponding position in the diagram will be empty. Software 85 Cultivation Time Chart Creating a CTC View 5 Cultivation Time Chart In the Cultivation Time Chart (cultivation progress/result diagram), the growth patterns of cell cultures can be graphically evaluated. It is also possible to export and print out the data. The CTC Views window required for creating a Cultivation Time Chart is opened by clicking on the CTC button in the Shortcuts area of the Cedex Control Center or by selecting the Cultivation Time Chart option in the Measurements menu. In the CTC Views window, charts can be created, viewed, edited, exported and deleted. A collection of data used for the creation of a particular chart is called a View. Each View can have up to 5 separate series of measurements for comparison of data. 5.1 Creating a CTC View The CTC Views window has two areas (see Figure 61): D The View area is used for viewing, exporting, creating and deleting charts. The Filter By section located at the top of this area is used for finding previously created cultivation time charts. The Series belonging to selected view area is used for creating, editing, listing or deleting the various measurement series belonging to the View highlighted in the View area. Figure 61: CTC Views window 86 Cedex Analyzer Operator’s Guide Cultivation Time Chart Creating a CTC View 5.1.1. The View Area This area is used for viewing, exporting, creating or deleting a View. If no filters have been set, all Views that have been created will be displayed under the View Name column. If filters have been set, only those Views that match those filters will appear under this column. To see the chart for a particular View, highlight the row of the desired view and click on the View Chart button. To create a new View, click on the button New. Highlighted rows of Views can also be exported with the Export button or deleted using the Delete button. Previously created views can be searched for using various filter criteria in the Filter By section at the top of the View area. One can filter by name of the View, username of the creator or by the date a View was created or modified. Enter the desired parameters and click on the Find button. When searching by date, the check-box next to the date must first be checked. After checking the box, clicking on the drop-down menu to the right of the date will open up a calendar in which the desired date can be selected. When the button New is selected, a window will open asking for a name for the new View. A name must be given before a View can be created. Give a name for the new View and click on OK. The new View will appear highlighted in the left-hand section of the View window. It is now possible to select the desired measurements for this View using the Series belonging to selected view area at the bottom half of the CTC Views window. 5.1.2. The Series of Measurements Belonging to Selected View Area This area is used for creating, editing, viewing and deleting measurement series for a particular View. In order add to or modify specific measurement series for a particular View, that View must be highlighted in the View area. Software D 87 Cultivation Time Chart Creating a CTC View 5.1.3. Adding Measurements to a View Do the following to find and select measurements for a new View or for a View that has already been created: D 1 Highlight the View to be modified in the View area of the CTC Views window and click on the New button on the right-hand side of the Series belonging to the selected view area. This will open the Selection of Data Series window, in which measurements can be selected for the creation of a View (see Figure 62). 2 Choose the desired System name in case measurements from other systems that have been imported into the database should be added to the chart (see “Data Exchange”). 3 Choose the Workarea (base directory in which measurement data are stored), the Reactor ID and the preferred Data Set (original or effective measurement data, see “Effective Data Sets”). 4 Click on the Find button. All of the Sample IDs associated with that particular Reactor ID will appear in the upper section of the Selection of Data Series window. 5 Click on the empty column to the left of the measurement to be added to the series in order to highlight that measurement. Multiple measurements can be highlighted either by holding down the or key. 6 When all of the desired measurements have been selected, click on the Add selected measurements button. 7 Click on Save. The Selection of Data Series window will automatically close. The CTC Views window will reappear and show the measurements that have been added to the View in the Series belonging to the selected view area. 8 To add another series to a View, click on the New button again. The Selection of Data Series window will open. Follow steps 2 – 7 above to add measurements to the new series. 9 Up to 5 separate series can be added to one View. Once 5 series have been added to a View, the New button will no longer be available for that View. ■ Figure 62: Selection of Data Series window 88 Cedex Analyzer Operator’s Guide Cultivation Time Chart Creating a CTC View 5.1.4. Editing Measurements in a View Measurements can be added or removed from a particular View by using the Edit button in the Series belonging to the selected view area of the CTC Views window. To edit the measurements found in a View, do the following: 1 Highlight the row of the View to be edited in the View area of the CTC Views window. 2 Highlight the particular series of a View to be edited in the Series belonging to the selected view area. 3 Click on the Edit button. This will open the Selection of Data Series window (see Figure 62). 4 Add or remove measurements from the series list by highlighting the measurements and clicking on the Remove button at the bottom of the window. 5 Click on the Save button. The changes will be saved and the window will automatically close. 6 The CTC Views window will become available and other series in the same View or else other Views can now be edited. ■ Measurements can also be excluded from a cultivation time chart without being removed from the series. All measurements selected for a series that are marked with a (✔) in the checkbox of the Use column will be displayed in the Cultivation Time Chart. Should it not be desirable to display a particular single measurement, the measurement can be unselected by removing the (✔) in the Use column with a mouse click. 5.1.5. Viewing List of Measurements in a Series If measurements have been added to a View, a simplified list of the series will appear in the left-hand side of the Series belonging to the selected view area of the CTC Views window. To see the full list of all measurements from all series created, click on the List button. This will open the Series List window (see Figure 63). A search for specific measurements in the list can be done using the Filter By area in the upper right-hand corner of the Series List window. Searches can be made by Workarea, Reactor ID or date of measurement. Once the filter parameters have been set, click on the Find button. The measurements that fit the parameters will be displayed in the Measurements area in the lower left-hand corner. Only series that contain measurements with the correct parameters will be displayed in the Series area in the upper left-hand corner of the Series List window. D Figure 63: Series List window Software 89 Cultivation Time Chart Creating a Cultivation Time Chart 5.1.6. Deleting Views and Series Entire Views can be deleted by highlighting the View and clicking on the Delete button in the View area of the CTC Views window. If one series of a particular View should be deleted, highlight the relevant View in the View area, then highlight the series to be deleted in the Series belonging to the selected view area. Click on the Delete button in the Series belonging to the selected view area of the CTC Views window. 5.1.7. Exporting a View The series of measurements in a view can be exported via the Export button in the CTC Views window. Select the View to be exported in the View area of the CTC Views window and click on the Export button. An Export window will open in which the desired settings and parameters can be selected (see “Export to file”). 5.2 Creating a Cultivation Time Chart Once a View has been created with the desired series of measurements to be used for a chart, the Cultivation Time Chart can be created. To create a Cultivation Time Chart, do the following: D 1 Highlight the View to be used for the creation of a Cultivation Time Chart in the CTC Views window. 2 Click on the View Chart button, this will open the Cultivation Time Chart window (see Figure 64). 3 Select the parameters to be displayed in the chart by clicking on the desired parameters in the Data Selection area in the upper right-hand corner of the window (see “The Data Selection Area”). 4 Select the series to be displayed in the Chart area in the lower right-hand corner of the window. 5 A graph will then be generated showing the selected parameters and series. ■ Only measurements already loaded will be displayed in the Cultivation Time Chart window diagram. The Selection of Data Series window must be brought up again to add additional measurements. 90 Cedex Analyzer Operator’s Guide Cultivation Time Chart Creating a Cultivation Time Chart 5.2.1. The Data Selection Area Which curves should be displayed in the diagram is determined in the Data Selection area of the Cultivation Time Chart window. The following values can be selected for display: Viable Cell Conc.: Viable cell concentration[cells/ml] Total Cell Conc.: Total cell concentration [cells/ml] Viability [%]: Percent viability Total Cell Count: Total number of all cells counted Avg. Compactness: Average compactness of living cells [without unit] Avg. Diameter: Average diameter of living cells [µm] Std. Dev.: The deviation from image to image of the number of cells found in each image Aggregate Rate [%]: Percent of cells found in aggregates Dead Cell Conc.: Dead cell concentration [cells/ml] Viable Cell Count: The total number of viable cells counted Dead Cell Count: The total number of dead cells counted Total Object: The total number of objects counted D Click on the appropriate checkboxes to select the desired values. Figure 64: Cultivation Time Chart window The measurement series, including information about which measurements have been used to create the chart, are listed in the Data Series area in the bottom left-hand corner of the Cultivation Time Chart window. A legend indicating the symbol (form and color) used for each parameter is at the top of the graph. The color used for each series is indicated in the Chart area in the lower right-hand corner of the window. The x-axis units can be displayed as either days [d] or hours [h]. Click on the Time[d] below the x-axis to switch to hours. The x-axis calibration will be automatically recalculated. Software 91 Cultivation Time Chart Creating a Cultivation Time Chart If the mouse pointer is placed over a measurement point in the diagram, detailed information, including the date and time of the measurement as well as the results, will be displayed next to the point. Also, the graphic representation can be enlarged or scaled down again with the use of the mouse (see “Enlarging the Diagrams”). 5.2.2. Fitting to the Lowest Common Value The Fit lowest common value button enables automatic shifting of the zero-point of single measurement series to each other. The following can be selected: Viable Cell Density Dead Cell Density Total Cell Density By means of this function, the zero-point of each series will automatically be shifted on the x-axis, in order to be able to better compare the measurement series to each other. The lowest common value of all the measurement series is automatically determined, and the graphs in the diagram are shifted to each other so that the lowest common value falls on the x-axis at the same point. While doing so, the left-most point of the graph of all the measurement points is set at value 0. D 5.2.3. Measurement Series Offset In the graph, measurement series are automatically displayed such that all measurement series begin at time 0. The different measurement series can, however, be best compared to each other when the beginning of the exponential growth phase (log phase) starts at the same time. Therefore, it is possible to shift the curves in the diagram by changing the offset for each series. A button in the Offset column of the Data Series area displays the offset set by the user (the button displays 0 [h], if an offset was not set). Clicking on this button opens the Measurement Offset window. The measurement series offset can be then manually shifted in this window. Figure 65: The Measurement Offset window The offset can be separately entered for each of the five measurement series by clicking the button with the corresponding number of the measurement series. Large time differences can be entered in days [d], small ones in hours [h] by clicking on the appropriate buttons [d]/[h]. The offset can be set by selecting the desired series number (colored boxes) and then moving the slider to the desired offset. Using the slider will cause an immediate shift of the measurement series in the diagram so that it can be immediately seen where the best position for a series is in the diagram. The smallest time unit that can be set is 0.10 hours. The OK button confirms the offset values in the graphics. 92 Cedex Analyzer Operator’s Guide Cultivation Time Chart Creating a Cultivation Time Chart 5.2.4. Variable Axis Calibration The buttons lin and log are used to determine whether the y-axis should display in a linear (lin) or logarithmic (log) scaling for cell concentration data. The default value is lin. The x-axis units can be displayed as either days [d] or hours [h]. Click on the Time[d] below the x-axis to switch to hours. The x-axis calibration and division will be automatically adjusted. 5.2.5. The Exponential Regression Button Using the Exponential Regression button in the View section of the CTC Views window, cell culture growth patterns can be displayed with their Specific Growth Rate [µ] and Doubling Time [T]. The corresponding values appear in the Data Series list (see Figure 66, below). D Figure 66: A view of the Exponential Regression window Only viable cell concentration will be shown in this graph. The measurement parameters Specific Growth Rate [µ] and Doubling Time [T] of the culture are computed by means of the differential curve. Click on the 5.2.6. to close the Exponential Regression window. The CTC Views window will reappear. Printing out a Cultivation Time Chart Cultivation Time Charts can be printed out via the Print button in the Cultivation Time Chart and the Exponential Regression window. To print out a chart, click on the Print button. A window will open in which the printer settings can be selected or the chart can be directly printed. Clicking on the Print button will open a window with a preview of the page to be printed. Software 93 General Functions of the System Data Management 6 General Functions of the System The Cedex Control Center offers users with the appropriate rights access to a set of functions in addition to the basic functions of analyzing, modifying and reprocessing samples and measurement results. These functions allow for easy and user-friendly operations with the Control Center, although some functions are only available to the Administrator (see “Administrator Functions”). 6.1 Data Management 6.1.1. Printing Reports The main Report menu is located directly on the menu-bar of the Cedex Control Center; this menu serves as direct access to the report functionality for all of the different reports. In addition, Print Report buttons can be found in all of the appropriate windows (e.g., Measurement List, Audit Trail etc.). Pre-configured report templates can be selected for printing reports, and new templates can be created. The following information can be printed out: D Operational data Allows the user to track a device’s operating hours, number of measurements and liquid consumption. Measurement data Contains information about measurement parameters and calculated results, e.g., sample identification data, name and parameters of the Cell Type used, calculated measurement result data etc. Select the desired option for the form in which the result data should be printed via the Name drop-down menu in the Report Template for the measurement report. Options include: Standard (standard measurement report without details) Full Details (full report including detailed images, results and histograms) List (for multiple measurements displayed in a list) Measurement audit trail (measurement report with audit trail entries) Multiple long (for multiple measurements printed one after the other) System configuration parameters Provides a list of system parameters as displayed in the System Options. Audit trail Provides a statement of all user initiated activities and related data. Automatic adjustment and alignment verification Presents results from the automatic adjustment of focus and brightness. 94 Cedex Analyzer Operator’s Guide General Functions of the System Data Management 6.1.2. Export to file Exporting data is done via the Export to file area of the Measurement List window or via the Export to file option in the Functions menu of the Control Center. Four different formats can be chosen including CSV, XML, Excel-DIF and Flat file. In addition, a sub-set of parameters to be included in the file can be selected. To export measurement results, follow the instructions below: 1 Select the Export to file option in the Functions menu of the Control Center. The Measurement List window will appear with the Export To File button located at the bottom of the window. 2 Select a single measurement from the list by clicking on the field to the left of the desired line. To choose a set of measurements, hold down the Ctrl button while selecting the appropriate lines. Alternatively, the desired measurements can be searched for using different filter criteria (see “Searching for measurements”). 3 Click on the Export To File button. The Export window will open. 4 In the Export window, individual Parameter and String delimiters can be defined (this only applies to CSV and Flat files). 5 In the Location area, the target path to be used for storage of the export file is entered. The button on the right of the entry field opens a window in which the path can be directly selected. The name of the file will be automatically generated. 6 To specify a sub-set of parameters to be exported, either click the check-boxes beside the preset options (i.e., All Parameters, Cell Data and Overall Results) or select the desired parameters from the Columns to Export area. To choose a set of parameters, keep the button pressed while making selections. The preset options are: D All Parameters: All parameters about the measurement. Cell Data: Data for each and every cell and object detected in the measurement. Overall Results: Results such as average cell diameter, %viability, total cell concentration, viable cell concentration, etc. 7 In the File format area, select the file format by clicking on the appropriate check-boxes. The files will automatically and unchangeably receive .dif or .csv file name extensions. The file format Excel-DIF should always be chosen if a file is to be exported into Excel. 8 Click on the Export Selected Data button. 9 A message window will appear to confirm successful export of information. Click on OK. ■ The measurement data can then be viewed in the file created. Figure 67: The Export window 6.2 Data Exchange The Data Exchange function allows for the exchange of measurement data between different Cedex Software 2.2 System databases (DBs). The user can export selected data from one Cedex Software 2.2 System DB and import it into another. Software 95 General Functions of the System Data Exchange 6.2.1. Export In order to exchange data between systems, the data first needs to be exported from the system on which it was created to external storage. To export data, proceed as follows: D 1 Select the Data Exchange option in the Functions menu of the Cedex Control Center. 2 Select Export. The Measurement List window will appear with an Export To DB button located at the bottom of the window. 3 Select a single measurement from the list by clicking on the field to the left of the appropriate line. To choose a set of measurements, hold down the button while selecting the appropriate lines. Alternatively, the desired measurements can be searched for using filter criteria. 4 Click on Export To DB to open the Export To External DB window. 5 Enter the path under which the export file should be stored in the Location area. Alternatively, the button on the right of the entry field opens a window in which the path of the database file can be directly selected. Click on OK. The Export To External DB window will reappear. 6 Click on Export to start the exporting process. A message window will appear as soon as export has been successfully completed. Click on OK. 7 Close the Export To External DB window by clicking on . ■ A default entry for the path under which the export file should be stored can be entered in the System Options under the Setup menu. Open the Data Exchange tab and look for the ExportPath parameter. In the Value column, enter the default path (see list of User Preferences and System Options in the Appendix). The following message may appear after selecting the measurements to be exported and clicking on the Export button: Figure 68 If this message appears, click on Yes to confirm the message and install the certificate. The export will continue after confirming the installation of the certificate. 96 Cedex Analyzer Operator’s Guide General Functions of the System Viewing and Evaluating the Audit Trail File 6.2.2. Import Once measurement data has been exported from one system to external storage, the data can then be imported to another system. To import measurement data into a Cedex Software 2.2 database, follow the instructions below: 1 Select the Data Exchange option in the Functions menu on the Cedex Control Center. 2 Click on Import to open the Import From External DB window. 3 Enter the path of the file to be imported in the Location area. Alternatively, the button on the right of the entry field opens a window in which the path of the file can be directly selected. Click on Open. The Import From External DB window will reappear. 4 Click on the Import button to start the import process. A message window will appear when the import is successfully completed. Click on OK. 5 Close the Import From External DB window by clicking on . ■ It is not possible to import more than 200 measurements at one time. A default entry for the path under which the import file should be stored can be entered in the System Options under the Setup menu. Open the Data Exchange tab and look for the ImportPath parameter. In the Value column, enter the default path. To view imported measurements that come from a different system and, consequently, have a different System ID, select the appropriate System ID name for those measurements in the SystemName dropdown menu in the Measurement List window. 6.3 D Viewing and Evaluating the Audit Trail File The Cedex Analyzer software automatically creates an Audit Trail (log) file for each sample and records all relevant hardware information relating to the sample. The Audit Trail file data can never be overwritten. This ensures that all recorded, analyzed and modified measurement data is documented (see “The System Audit Trail File”). Software 97 General Functions of the System User Preferences 6.4 User Preferences The User Preferences window is located under the Master Data drop-down file menu in the Cedex Control Center (see Figure 69, below). A logged-in user with specific access rights to the User Preferences option can set preferences for a number of elements including the result parameters to be displayed in the Multi Run result list and Measurement List window and default measurement parameters for carrying out measurements. Figure 69: User Preferences window with the tab Measurement List Default Filter selected D 6.4.1. Adjusting Result Display in the Measurement List and Multi Run windows The result data to be displayed in the Measurement List window, as well as the result list area of the Multi Run window, can be adjusted in the User Preferences window. The numbers in the entry ResultsToShowInList located under the Measurement List Default Filter tab indicate which types of results will be displayed in the Measurement List. The numbers in the entry DisplayedResultTypes under the General tab indicate which types of results will be displayed in the result list of the Multi Run window as follows: 1: Avg Diameter 5: Avg Compactness 6: Viable Cell Count 7: Dead Cell Count 8: Total Object Count 9: % Viability 10: Viable Cell Conc. 11: Dead Cell Conc. 12: Total Cell Conc. 13: Std. Deviation 14: Total Cell Count 15: % Aggregate Rate The default entry for these fields is 12, 10, 9, which corresponds to Total Cell Conc., Viable Cell Conc. and % Viability, respectively. The order in which the numbers are listed is the order in which the results will appear in the lists. To add more results to be displayed, enter the number that corresponds to the desired result parameter in the fields. Numbers must be separated by a comma with no space in between. 98 Cedex Analyzer Operator’s Guide General Functions of the System User Preferences 6.4.2. Specifying Default Measurement Parameters The logged-in user with specific access rights to the User Preferences option in the Master Data menu, can determine the preferred default values for certain measurement parameters (Cell Type, dilution, etc.). The default parameter settings are only valid for this user. Follow the instructions below to change the default values for certain measurement parameters: 1 Select User Preferences in the Master Data menu of the Control Center. This will open the User Preferences window. 2 Select the Measurement tab in the User Preferences window. 3 Manually type in the appropriate default measurement parameters in the Value column. The defaults for the following parameters can be determined: CellType, DefaultCombinedNumber (for the Measurement Statistics Histogram), MeasurementPrecision, ReactorID, SampleInitialDilution, SampleVolume, Workarea. CellDiameterHistogramDividers (sets the intervals to be applied to all cell diameter histograms; note that the format should be x y z). If the numbers are placed in brackets, such as (x) (y) (z), the intervals will be shown in the histogram by default, but not activated. 4 Put a check mark in the check-box of the Save Last column if the last value used for a measurement should be used as the default for the next measurement. 5 Click on Save to confirm. 6 Close the window. The new default parameters will apply to new measurements. D ■ 6.4.3. Specifying Other Default Parameters Other default parameters can be specified for the Measurement List window, the CTC Views window and the Audit Trail. Select the following tabs to create or alter default parameters: Measurement Default Filter: Create or alter default parameters for filter settings in the Measurement List window. CTC Views Default Filter: Create or alter default parameters for the filter settings in the CTC Views window. Audit Trail Default Filter: Create or alter default parameters for the filter settings in the Audit Trail window. Software 99 General Functions of the System Changing own Password 6.4.4. Specifying the Workarea for the Analysis Data The analysis results are stored in the workarea that is selected in the Measurement window before a measurement is run. If analysis results from a specific workarea are to be viewed, the appropriate workarea needs to be chosen from the drop-down list in the Measurement List window. The user can only choose a workarea from the list of workareas to which she/he has been assigned. Only the Administrator has the right to assign workareas (see “Administration of User Accounts”). 6.5 Changing own Password Users may change their own passwords. Follow the instructions below: D 100 1 Click on the System menu on the Control Center. 2 Click on Change my Password; the Change password area will appear. 3 Enter your present password in the first field. 4 Enter your new password in the second and third fields. 5 Click on OK to confirm the entry, and a message will confirm the entry. 6 Click on OK to shut the window. ■ Cedex Analyzer Operator’s Guide Administrator Functions Administration of User Accounts 7 Administrator Functions The following system functions are generally only available to the Administrator and/or Superuser: Administration of user accounts Password management and assigning workareas Adjustment of the image analysis Securing data 7.1 Administration of User Accounts The user usually has limited access rights. All administration rights relating to user accounts, i.e., creating, deleting, modifying and delegating rights, should remain exclusively with the Administrator. All administration of user accounts and rights management is done in the User Rights Management area. To open the User Rights Management area, click on the Setup menu in the Cedex Control Center and select User and Rights Management. The User Rights Management window is structured with menus and sub-menus similar to the directories in Windows Explorer (see Figure 70). The distinction between functions, roles, users and groups, which is mainly connected to the delegation of rights, is explained in the appropriate sections of this chapter. Password settings can also be configured in this area. 7.1.1. Creating User Accounts D Before creating new user accounts, the password configurations should be set up (see “Password Management”). Follow the instructions below to create a user account: 1 Click on the Setup menu in the Cedex Control Center. 2 Click on User and Rights Management; the User Rights Management window will appear. 3 Right click on the All Users folder and click on Create new user. The User account area will appear. 4 Enter the user’s first name and last name in the first and second rows and a username for the account in the third row. 5 Enter a temporary password for this user account in the fourth field. Click on Save to confirm. If the option, “must change on first login” is selected, the user will be forced to change the password the first time he or she logs into the Control Center. 6 Restart the Cedex Software 2.2 application. ■ A user is only authorized to carry out measurements after he has been assigned at least one work area. Software 101 Administrator Functions Administration of User Accounts 7.1.2. Assigning Access Rights The user is normally denied access rights to certain areas, e.g., administration of user accounts and sensitive system functions (focus adjustment, creating SST-Checkpoints etc.). The user, therefore, cannot access all of the menus on the Control Center after login. Access rights can be modified at any time by the Administrator. Rights are generalized in user roles that can comprise a single access right or a set of access rights. To grant rights you will need to assign one or more user roles to a user. The following user roles are available after installation of the software: Administrator Production Staff Research Staff Superuser Support By default, the pre-installed Production Staff, Research Staff and Support roles have no functions assigned to them. More detailed information about creating functions for each pre-set user role, as well as editing existing functions and creating new user roles, can be found under “Creating and Editing User roles”. D Follow the instructions below to assign rights to a user account: 1 Click on the Setup menu in the Cedex Control Center. 2 Click on User and Rights Management, and the User Rights Management window will appear. 3 In the All Users main menu open the user account menu that is to be modified. A User Role sub-menu will appear. 4 Open the All Roles main menu and drag the appropriate user role from the All Roles menu into the All Users sub-menu. The access rights available for this user role will be added to the account. To deny certain access rights, the corresponding user role needs to be deleted from the All Users sub-menu. Right click the user role which is to be deleted and click on Remove the role from the user. ■ Figure 70: User Rights Management area 102 Cedex Analyzer Operator’s Guide Administrator Functions Administration of User Accounts 7.1.3. Creating user groups IIt is possible to generalize one or more user accounts in user groups. Instead of assigning rights to a single user, a user role or a set of user roles can be assigned to a user group. The whole user group, therefore, receives all access rights that have been assigned to the user roles. To create a user group and add user accounts proceed as follows: 1 In the User Rights Management area right click on the User Groups main menu and click on Create new user group. 2 A name for the new group can be entered in the User Group window. 3 Click on OK to add user group to User Groups list. 4 Open the All Users main menu and drag from it the desired user account into the appropriate user group sub-menu. The user is added to the user group and receives all access rights assigned to this group. A user can be added to one or more user groups. ■ 7.1.4. Editing and Deleting User Accounts The first name, last name and username of a user account can be edited if, for example, an existing user is to be replaced by a new user with identical access rights. A user account can also be deleted in the editing area. Proceed as follows to edit a user account: 1 Click on User and Rights Management, and the User Rights Management window will appear. 2 Open the All Users main menu and right click the user account menu to be edited. 3 Click on Edit the user and the User Account window will appear. The name, last name, username, password and priority can be changed. 4 Click on the Deleted check box if the user account is to be deleted. 5 Click on Save to store the changes. D ■ In order to avoid confusion, the software will not allow for the creation of a new user with the same user name as a user name that has been deleted. Measurements that have been run under a user name that has been deleted are still available for viewing. Software 103 Administrator Functions Administration of User Accounts 7.1.5. Creating and Editing User roles Rights are generalized in user roles that comprise a single access right or a set of access rights. In the User Rights Management area, access rights are declared as functions. It is necessary to determine the different responsibilities for the different roles and, therefore, functions they should have access to. Five standard user roles are pre-installed by the software. All of the roles are suggested roles that could be used for setting up specific distribution of access rights: Administrator: The administrator is allowed to use all administrative functions of the system. He is not allowed to use any operational functions. Production staff: It is intended for members of the production staff who are only allowed to use specific operational functions depending on company policies (i.e., execute measurements, execute an SST, change consumables). Research staff: Members of the research staff who could be allowed to use all operational functions of the system. Superuser: The Superuser is allowed to use all operational functions of the system mainly for maintenance purposes. Support: Support of the Cedex System by Roche technical services requires access to all operational functions similar to the Superuser role. D Access to the System Options should be restricted to the Administrator, Superuser and Support. All options necessary for a user to modify his workplace according to his needs can be found under User Preferences. Only selected users should be authorized to edit SST-Checkpoints. See “Creating SST checkpoints” for further information. Follow the instructions below to create a new user role: 1 In the User Rights Management window right click on the All Roles main menu and then click on Create new role. 2 A name for the new role can be entered in the Role window. 3 Click on OK to add the new user role to the All Roles list. ■ To add rights to or delete rights from an existing user role proceed as follows: 1 Open the user role menu that is to be modified in the All Roles main menu. A Role Functions sub-menu will appear. 2 Open the All Functions main menu and drag from it the desired functions into the Role Functions submenu. These functions will be added to the user role. To delete certain functions from the User Role submenu, right click on the desired function and select Remove the function from the role. ■ 104 Cedex Analyzer Operator’s Guide Administrator Functions Password Management 7.2 Password Management The Cedex Software 2.2 has been equipped with a detailed password management that is compliant with CFR 21 Part 11 guidelines. 7.2.1. Specifying Password Characteristics Password settings can be specified and changed in the User Rights Management window. The following password settings can be configured: Composition rules Min characters /Min digits Minimum requirements for the number of characters and digits used Min length /Max length Minimum and maximum length of the password Attempts to login Number of times wrong passwords can be entered consecutively before this user is denied access. Only the Administrator can reverse denial of access by issuing a new password. The user will be warned before the last allowed attempt. Password … never expires Passwords never lose their validity. expires in number of days after which passwords lose validity Warn the user Number of days before password expiration to warn the user Old password can be reused after Number of new passwords that must be used before old password can be reused Use blacklist The so-called BlackList can be used to restrict selection of passwords to only those that fulfill a specific security standard. This list contains passwords that are not allowed to be used. The list is empty after installation of the software by default. D The Administrator can enter incorrect passwords without limits with an extended time period after each retry. 7.2.2. Assigning New Passwords Follow the instructions below: 1 Click on User and Rights Management, and the User Rights Management window will appear. 2 Open the All Users main menu and right click on the user account menu that is to be edited. 3 Click on Edit the user and the User Account window will appear. 4 Enter new password in the corresponding line (Password). 5 Click on Save to store the change. ■ Software 105 Administrator Functions Assigning Work Areas 7.3 Assigning Work Areas The analysis results from a measurement are organized in work areas. A user needs to be assigned to at least one work area to be able to run a measurement, otherwise an error message will appear. All measurement data produced by this user will be saved in the work area selected during execution of measurements. The user can only work with measurement data from work areas to which he has been assigned. New work areas can be created and assigned to one or more users via the User Rights Management area. Follow the instructions below to create and delegate work areas: 1 Click on the Setup menu on the Cedex Control Center. 2 Click on User and Rights Management. The User Rights Management window will appear. 3 In the All Users main menu, open the user account menu that is to be assigned the work area. A User Workareas sub-menu will become available. 4 Open the All Workareas main menu and drag the desired work area into the User Workareas sub-menu. This work area will be added to the user account. ■ To later deny access to a work area, follow the instructions below: D 106 1 Open the User Workareas sub-menu in the user account that is to be modified. 2 Right click on the work area that is to be removed and click on Remove the workarea from the user. ■ Cedex Analyzer Operator’s Guide Administrator Functions The System Options 7.4 The System Options The System Options area, in which system parameters are configured, is located in the Setup menu on the Cedex Control Center. Only those users who have been given access to the System Options function (for example the Superuser and Support) can change system parameters. Setting system parameters includes several changes and modifications, some of which are explained in detail in the sections below. The parameters are organized based on the application areas that are affected (e.g., Measurement, Hardware, Data Exchange). See “System Options and User Preferences” in the Appendix for a detailed description of all of the System Options. The Cedex Software 2.2 may need to be restarted in order for changes in the Systems Options to take effect. All elements in the System Options that have not been explicitly described in this Operator’s Guide must not be changed without prior arrangement Roche Diagnostics GmbH. In all cases, contact must be made with the local Roche technical services before any such changes are made. Access to the Systems Options should be restricted to only the users who are responsible for maintenance of the system! Changing default values in the Systems Options window can have an adverse effect on the system and measurement results! 7.4.1. Automatically Start the Hardware Management If the AutomaticallyStartHardware parameter is active (entry “1” in the Value column) the hardware management will automatically be initialized when the software is started. To turn off this function, set the value to “0” in the Value column. 7.4.2. D Modifying the Standard Setting for the Multi Sampler DefaultCup The default setting for the Multi Sampler DefaultCup (Cedex Sample Cup used for Prime, LM ShutDown, focus calibration and all cleaning routines) is position 1 on the Multi Sample tray. The default position can be changed to any other position. To change the position for the DefaultCup location, do the following: 1 Open the System Options window and click on the General tab. 2 Look for the parameter DefaultCupPosition. The number entered in the Value column will determine the position for the DefaultCup on the multi sampler tray. 3 Click on Save to confirm the change. ■ The position chosen for the Multi Sampler DefaultCup does not influence measurements. All 20 positions on the sampler plate can be used for measurements. Should a sample be present in the DefaultCup position during Prime, LM ShutDown, calibration or any cleaning routines, it can no longer be used for measurements. Software 107 Administrator Functions The System Options 7.4.3. Turning off Automatic Incrementation of Sample Cup Position In the case of single measurements run via the Measurement window on a Cedex Analyzer with a Multi Sampler attached, the software will automatically incrementally increase the sample cup position number with each new measurement. To switch off this feature, do the following: 1 Open the Systems Options window and click on the Measurement tab. 2 Look for the parameter SuggestNextCupPosition. 3 Select 0 from the drop-down menu to turn off the feature. 4 Click on Save to confirm the change. ■ When 0 has been selected, the suggested cup position will always be the same. 7.4.4. D Error Level Displayed to Users Errors in the software and hardware will be displayed to the user in the form of an error message. The level of error that will result in the display of an error message depends on the setting of the parameter ErrorLevelDisplayToUser in the General tab of the Systems Options window. The following levels are available: Level 1 (Fatal): fatal error, system/hardware crash. Level 2 (Critical): Error as a result of invalid measurement. Level 3 (Error): Error, but the result does not cause an invalid measurement. Level 4 (Warning): Information for user. If, for example, the ErrorLevelDisplayToUser is set at Level 1, only error messages regarding system or hardware crashes will be displayed to users. The factory-installed default for the ErrorLevelDisplayToUser is set at Level 3 (Error). 7.4.5. Liquid Container Configuration In the Liquid Container Configuration area, the minimum and maximum liquid levels for reagent and waste containers can be set. To open the Liquid Container Configuration window proceed as follows: 1 Click on the Master Data menu on the Cedex Control Center. 2 Click on Liquid Container Configuration and the window will appear. ■ Maximum and minimum volumes can be defined using this window. When standard sized containers are used, it is not advisable to change default settings for the Min volume and Max volume. It is also possible to define a Warn Level and a Lock Level. The standard default for the Warn Level is 6. This means that a warning message will appear if the amount of reagents left is 6 ml or less. The standard setting for the Lock Level is 3, which means that the system will be locked (i.e., no further measurements will be possible) if there are only 3 ml left. The settings for the Warn Level and Lock Level can be changed. Saving changes will immediately update the estimation of the number of remaining measurements. 108 Cedex Analyzer Operator’s Guide Administrator Functions Adjustment of the Image Analysis using the Live Operator 7.4.6. Disabling the Reagent Control The Reagent Control function keeps track of the amount of reagents used and notifies the user when the levels are running low. The function can be disabled in the General tab of the System Options window. The Reagent Control function is enabled when the value for the DisableReagentControl entry is set to “0”. To disable the function, set the value to “1”. 7.4.7. Default Settings In general, research or production staff users are not assigned access rights to the System Options window in which default settings that apply to the whole system can be configured. However, some parameters needed to customize the individual workplace (e.g., definition of the default settings for certain measurement parameters) can be found under User Preferences (see “User Preferences”). 7.5 Adjustment of the Image Analysis using the Live Operator The Cell Type (operator) selected for a measurement takes care of the image evaluation. Roche Diagnostics GmbH has put in one pre-setting: Std. Size (V5.00) for normal-sized cells with a diameter of about 12 µm, e.g., HB58 Individual adjustments of the operator can be helpful or necessary for cell cultures that, for instance, have an unusual optical appearance or for a counting strategy that deviates from the Cedex Analyzer (e.g., counting aggregates differently). D Adjustment of the operator is referred to as creating a new Cell Type. A new Cell Type can be created or an already existing Cell Type can be re-adjusted. This can be done with the help of eight parameters that influence the way in which an image is evaluated. Each of these parameters directly influences the image processing strategy and, hence, the measurement results. In the available software version, an algorithm with the pre-setting mentioned above is available. The parameters of the factory installed pre-setting are overwritable. For data safety reasons the parameters of the factory installed pre-setting should not be altered. Since original settings are overwritable, caution ought to be advised for all authorized users. 7.5.1. Description of the Cell Type List and Live Operator The Live Operator window, in which Cell Types can be created and modified, is accessed in two ways: Via the Measurement window in the View mode. Via the Cell Type List option in the Master Data menu on the Control Center. Software 109 Administrator Functions Adjustment of the Image Analysis using the Live Operator 7.5.2. The Cell Type List Window To open the Live Operator window directly from the Measurement window when it is in the View mode, click on the Live Operator button located in the middle of the Measurement window. When the Cell Type List option in the Master Data menu is selected, the Cell Type List window will open (see Figure 71). There are several options in this window including: New: Create new Cell Types. Edit: Modify existing Cell Types. View: View existing Cell Types. Delete: Delete existing Cell Types. Live Operator: Open the Live Operator window. D Figure 71: Cell Type List window 110 Cedex Analyzer Operator’s Guide Administrator Functions Adjustment of the Image Analysis using the Live Operator 7.5.3. Creating a New Cell Type A new Cell Type must be created and saved via the Cell Type window before the Live Operator window can be opened for modification of that Cell Type. A new Cell Type can be created by following the instructions below: 1 Open the Cell Type List window. Highlight the existing Cell Type upon which the new Cell Type should be based. 2 Click on the New button. A message will appear asking if the new Cell Type should be based on the highlighted Cell Type in the list. Click on Yes. The Cell Type window will open (see Figure 72). The Live Operator button will be inactive at this time. 3 Fill in the information for: The name of the new Cell Type Sample preparation procedure (Std. is currently the only option) Focus Offset: the offset from the ideal focus point. The Focus Offset should be set to 0 to ensure best results for cell count and determination of viability. Please consult local Roche technical services before using any other number for the Focus Offset as selecting another value for this parameter may lead to poor results. Note that the Sedimentation Duration does not apply to the Cedex Standard Analyzer. Make sure that the IR Operator is set to CXStdImageOperator. 4 Click on the Save button. The Cell Type window will automatically close. The Cell Type List window will be active again and include the just-created Cell Type in the list. 5 Highlight the row of the new Cell Type and click on the Edit button. The Cell Type window will reopen and the Live Operator button will be active. 6 Click on the Live Operator button and the Live Operator window will open (see Figure 73). 7 In the Data Source area, select the Work Area, followed by the Reactor ID, Sample ID and Data Set of the measurement for which the image analysis should be improved. The parameters for the loaded measurement are preset. 8 Select an image of the measurement in the Image ID section. This image will be loaded and displayed in the window in the upper right-hand corner with the living cells marked with a green circle and the dead cells marked with a red circle. 9 Make the desired modifications on a single parameter first. As soon as a parameter has been modified, reprocessing of the data is automatic (see “Description of the Individual Operator Parameters”). The image display then shows the reprocessed image (see “Working with the Live Operator”). 10 When an optimized adjustment of the Operator parameters has been found, click on Save to confirm the modification for the new Cell Type. D ■ When Cancel is clicked on, the Live Operator window will close without saving the changes. Software 111 Administrator Functions Adjustment of the Image Analysis using the Live Operator 7.5.4. Editing an Existing Cell Type An existing Cell Type can be modified. However, it is NOT advisable for data safety reasons to modify an existing Cell Type that has been used for measurements. A new Cell Type based on an existing Cell Type should be created instead. Follow the instructions below to modify an existing Cell Type (not advisable!): 1 Select the Cell Type to be edited from the list of Cell Types at the top of the Cell Type List window and then click on the Edit button. The Cell Type window will open. 2 Modify the following information if desired: The name of the Cell Type Sample preparation procedure (Std. is currently the only option) Focus Offset D 3 Make sure that the IR Operator is set to CXStdImageOperator. 4 Click on the Live Operator button in order to modify other parameters within the Live Operator window for that Cell Type (see “Working with the Live Operator”). 5 In the Data Source area, select the Work Area, followed by the Reactor ID, Sample ID and Data Set of the measurement for which the image analysis should be improved. The parameters for the loaded measurement are preset. 6 Select an image of the measurement in the Image ID section. This image will be loaded and displayed in the window in the upper right-hand corner with the living cells marked with a green circle and the dead cells marked with a red circle. 7 Make the desired modifications on a single parameter first (see “Description of the Individual Operator Parameters”). As soon as a parameter has been modified, data reprocessing is automatic. The image display then shows the reprocessed image. 8 When an optimized adjustment of the Operator parameters has been found, click on Save to confirm the modifications. 9 Click on Cancel to close the window without saving any changes. ■ 7.5.5. Viewing an Existing Cell Type Select the Cell Type to be viewed from the list of Cell Types at the top of the Cell Type List window and then click on the View button. The Cell Type window will open in which the information for focus point (Focus Offset) and sedimentation time (Sedimentation Duration) can be viewed. Click on the Live Operator button in order to view other parameters within the Live Operator window for that Cell Type (see “Description of the Individual Operator Parameters”). 112 Cedex Analyzer Operator’s Guide Administrator Functions Adjustment of the Image Analysis using the Live Operator 7.5.6. Deleting an existing Cell Type Select the Cell Type to be deleted from the list of Cell Types at the top of the Cell Type List window and then click on the Delete button. A confirmation box will appear, asking the user if he/she wants to delete the Cell Type. If confirmed, the Cell Type will be deleted and disappear from the list. All parameters of the measurements are logged. Deleted Cell Types have no influence on future measurements, but the parameters of deleted Cell Types used for past measurements will still be appear in the printed reports of those measurements. D Figure 72: Cell Type window 7.5.7. Working with the Live Operator The Live Operator window can be opened via the Cell Type List window, the Cell Type window and the Measurement window. If the Live Operator button in a Measurement window containing specific results is clicked on, the Live Operator will open with the images of that measurement already loaded. If the Live Operator is opened via the Cell Type or Cell Type List windows, the first measurement in the Measurement List will be loaded. In the Live Operator window, some of the 8 parameters can be displayed on the screen at the same time. Parameters at first not visible can be scrolled into view using the scroll bar under the Operator Parameter display. The table below displays the positions and settings of the 8 Operator parameters. See also “Description of the Individual Operator Parameters” for a detailed description of each parameter. Software 113 Administrator Functions Adjustment of the Image Analysis using the Live Operator Identifier Minimum Maximum -20 20 0 40 250 110 DeadAppearance -10 10 0 DeadAggregateMin 250 1500 360 DeadAggregateMax 1500 5000 2250 DeadAggregateApp -10 10 0 0 20 7 5000 30000 5400 LivingAppearance DeadSize BorderWidth MinPollutionArea Std. Size (V5.00) Table 1: A list of the Operator parameters After loading a measurement (Reactor ID and Sample ID) and selecting an image, the selected image is displayed in the upper right-hand corner of the Live Operator window. Each single cell detected by the Cedex Analyzer is marked as dead (red circle) or living (green circle). D Figure 73: Setting parameters for Cell Type Standard Cells 114 Cedex Analyzer Operator’s Guide Administrator Functions Adjustment of the Image Analysis using the Live Operator In the Process Data area, the values for new and previous results are displayed for viable cells (the number of living cells of the current image), dead cells (the number of dead cells of the current image) and %viability. If an Operator parameter is modified, the newest values will appear under New column when an automatic reprocessing of the selected image is finished. The values of the previous processing are displayed under Previous column. Thus, direct comparison to each previous evaluation is possible. The labeling of the cells can be switched on and off in the upper-right hand corner in order to allow for better evaluation of the results from changes in parameter settings. If multiple parameter changes should be made at the same time, remove the check-mark in the Automatic process box by clicking on it. When the check-mark is removed, the button Process now becomes active. Make all changes then click on the Process now button for an analysis based on the new parameter settings. 7.5.8. Description of the Individual Operator Parameters LivingAppearance (Living Cells‘ Appearance) Range: [-20, 20], Default: 0, Unit: [absolute measure]. This parameter influences the recognition of living cells. When the value of this parameter is set high, contrastweak objects are also counted as living cells provided they additionally fulfill the size criterion. The lower this value is set, the more contrast an object must have for it to be counted as a viable cell. If the value is changed to positive, shadowy and greyish objects are increasingly counted as living cells. Such a change can be sensible if, for example, the optical image shows little contrast due to the structure of the medium or of the cells in the medium. D In standard situations a change of this parameter can result in the labeling of debris as cells! DeadSize (Dead Cells’ Size) Range [40, 250], Default 110, Unit [µm²]. Defines the minimum cross-sectional area of a particle in µm². Increasing this value means that fewer particles will be recognized as dead cells. DeadAppearance (Dead Cells’ Appearance) Range [-10, 10], Default 0, Unit [absolute measure]. This parameter influences the recognition of dead cells. If the value is set high, contrast-weak objects are also counted as dead cells as long as they additionally fulfill the size criterion. The lower this value is set, the sharper the contrast an object must have in order to be counted as a dead cell. DeadAggregateApp (Dead Cells’ Aggregate Appearance) Range [-10, 10], Default 0, Unit [absolute measure]. Defines the automatic evaluation of a dead cell aggregate (cluster).The cross-sectional area of dead cell aggregates are automatically partitioned into single cells. Increasing this value means that there are more single cells determined in the aggregate. Software 115 Administrator Functions Adjustment of the Image Analysis using the Live Operator DeadAggregateMax (Dead Cells’ Aggregate Maximum) Range [1500, 5000], Default 2250, Unit [µm²]. Defines the maximum cross-sectional area of a dead cell aggregate (cluster). The dead cell aggregate area within this range is automatically partitioned into single cells. Any aggregate larger than the specified maximum area is not taken into account. DeadAggregateMin (Dead Cells’ Aggregate Minimum) Range [250, 1500], Default 360, Unit [µm²]. Defines the minimum cross-sectional area of a dead cell aggregate (cluster). When this size is reached, it is then automatically partitioned into single cells. MinPollutionArea (Minimum Pollution Area) Range [5000, 30000], Default 5400, Unit [µm²]. Defines the minimum cross-sectional area of the pollution size e.g., debris particles, air bubbles etc. Any pollution size larger than the specified minimum area results in the entire image being excluded. D 116 BorderWidth [µm] Range: [0, 20], Default: 7, Unit: [pixels]. The border frame around the image not used for evaluation. The use of the sliders, especially in combination, can lead to unexpected results. Cedex Analyzer Operator’s Guide Administrator Functions Archiving Data 7.6 Archiving Data The objective of the archive function is to secure measurement data by exporting it to external storage media. Measurement data must be secured at regular intervals and thereafter deleted from the Cedex Analyzer Measurement List in order to ensure enough storage capacity on the Cedex Analyzer Control Unit. All data from a single or a set of measurements, or optionally only the images, can be deleted from the database once the measurement or measurements have been archived. Archiving should only be carried out by the administrator and selected users. Measurement data can later be restored from the archive, but restoring the data will only be possible using the Cedex System Database the data has been archived from. All data should also be backed up on a regular basis. Archiving does not replace a back-up strategy. Back-ups of the database should be carried out on a regular basis. 7.6.1. Archive To archive measurement data, proceed as follows: 1 Open the Functions menu in the Control Center and select the Archive function found within the Archiving menu. The Measurement List window will appear with an Archive button at the bottom of the window. 2 Select a single measurement from the list by clicking on the field on the left of the appropriate line. When choosing a set of measurements, hold the Ctrl button down while selecting the appropriate lines. In addition, the desired measurements can be searched for using various filters. 3 Clicking on Archive will open the Archive window. 4 The path under which the archive file should be stored is entered in the Location area. The button on the right of the entry field opens an explorer window in which the path can be selected directly. A file name for the data to be archived needs to be entered. Click on Save and the Archive window will reappear. 5 Click on the Archive button to start the archiving process. A message window will appear as soon as archiving of information is completed successfully. Click on OK. 6 Close the Archive window by clicking on D . ■ A default entry for the path under which the archive file should be stored can be entered in the System Options function under the Setup menu. Open the Data Exchange tab in the Systems Options window and look for the ArchivePath parameter. In the Value column enter the default path. The following message may appear after selecting the measurements to be archived and clicking on the Archive button: Figure 74 If this message appears, click on Yes to confirm the message and install the certificate. The archive will continue after confirming the installation of the certificate. Software 117 Administrator Functions Archiving Data 7.6.2. Restore To restore measurement data, follow the instructions below: 1 Open the Functions menu in the Control Center and go to the Archiving menu. 2 Click on the Restore function within the Archiving menu to open the Restore window. 3 The path of the file that is to be restored is entered in the Location area. The button on the right of the entry field opens an explorer window in which the path of the file can be selected directly. Click on Open and the Restore window will reappear. 4 Click on Restore to start the restoring process. A message window will appear as soon as the information has been restored successfully. Click on OK. 5 Close the Restore window by clicking on . ■ 7.6.3. D Deleting Archived Data Only data that has been archived can be deleted from the Cedex System Database. Archived data still located in the database can be searched for and displayed in the upper right-hand corner of the Measurement List window. Figure 75: Measurement List window with archived measurement shown To delete archived data, do the following: 1 Click on the Archived measurements(s) check box in the upper right-hand corner of the Measurement List window. 2 Click on Find to display archived measurements. Highlight measurements to be deleted by clicking on the field on the left of the appropriate line. When choosing a set of measurements, hold the Ctrl button down while selecting the appropriate lines. 3 Click the check-box beside Delete records if all measurement data is to be deleted from the system Database. If the option Delete only images is chosen, all data apart from the images will stay in the system Database. 4 Click on the Delete button to delete selected measurements from the Control Unit database. ■ 118 Cedex Analyzer Operator’s Guide E Maintenance and Care The analyzer should be regularly serviced to guarantee optimal performance and maximize the life span of the Cedex Analyzer. This includes the following maintenance procedures: Recurrent manual maintenance and cleaning routines when necessary. Cleaning routines with the Liquid Management. Cleaning and maintenance of the syringe module. Maintenance of the capillary tubes. Maintenance of the flow chamber, the microscope optic and the 8-way valve. This maintenance routine must be carried out only by an authorized service technician. This chapter provides detailed instructions and guidelines for each individual cleaning and maintenance procedure. E Maintenance and Care 119 Cleaning and Maintenance Check List 1 Cleaning and Maintenance Check List This checklist shows when each cleaning and maintenance routine should be done. Carry out these routines on a daily basis: LM Shutdown: always after the last measurement and before a Cedex Analyzer shutdown. If a Prime has been scheduled to be automatically run the next morning, the Hardware Management should not be shut down as a Prime can only be run when the Hardware Management is active (see “Scheduling Automatic Cleaning Routines”). Standard Clean: after the final measurement of a set of samples or before a longer pause between measurements. Chamber Clean 2: at least twice a day. Carry out this routine on a weekly basis: Intensive Clean Change of Trypan Blue solution The following routine should be done every week for users that refill reagents themselves: Empty the reagent containers and the waste container. Thoroughly clean the containers. Refill the reagent containers (see “Refilling Containers Individually“) Carry out this routine on a bi-monthly basis: Special Intensive Clean: at least twice a month with 0.1 – 1 N HCl instead of detergent. E 120 Carry out these routines on a regular basis (once a week or after 250 measurements): Clean the casing, Reagent Tray, Multi Sampler housing (if installed) and Reagent Port by wiping down with 70% alcohol and a lint-free cloth. Run a focus adjustment of the analyzer every month or after any change of position or vibration of the measurement system. Cedex Analyzer Operator’s Guide Scheduling Automatic Cleaning Routines 2 Scheduling Automatic Cleaning Routines Routine cleaning operations can be scheduled so that they are automatically included in the process queue. Depending on the settings, the cleaning operations are automatically run at a pre-defined time or after certain events. To create a new entry in the schedule, proceed as follows: 1 Select Scheduling from the Functions menu in the Control Center. The Schedule window will appear. 2 Click on New to open the Schedule process window. 3 Select the Process that is to be included in the schedule from the drop-down menu at the top of the window. The available processes include both cleaning routines (e.g., Fast Clean) and Hardware Management routines (e.g., Prime, LM Shutdown). 4 Select one of the three options with regard to the time schedule for an automatic process: Every: The process is automatically run at the selected interval of one or more days. A specific time of the day for operation can also be set. After an event: The process is automatically run after system start-up or after a selectable number of measurements. After certain time of inactivity: A certain amount of time of inactivity can be defined after which the process is run automatically. If the only once box is checked, the scheduled process will only be run once, even if there is another period of inactivity afterwards. 5 Click on Save to add the entry to the Schedule list. The Schedule process window will automatically close and the Scheduling window will reappear showing the newly scheduled process in the list. ■ Scheduled processes can also be edited and deleted by highlighting the appropriate row in the Schedule window and then clicking on the Edit or Delete buttons. Clicking on the Edit button will open the Schedule process window in which the process can be edited. When scheduling an LM Shutdown or a Prime, it is important to ensure that the Hardware Management is not shut down before the scheduled Prime or LM Shutdown is run (e.g., the hardware is shut down in the evening before a scheduled Prime is to be performed in the morning). Prime and LM Shutdown can only be executed if the Hardware Management is active. Maintenance and Care E 121 Daily and Manual Maintenance and Cleaning Routines Checking the Reagent Containers when Manually Refilling 3 Daily and Manual Maintenance and Cleaning Routines The following cleaning and maintenance routines should be carried out on a regular basis or whenever necessary. 3.1 Checking the Reagent Containers when Manually Refilling Empty reagent containers lead to wrong measurement results and can cause a dry run, thereby damaging the syringe and the 8-way valve. Regular checks of the liquid level are done via the Reagent Kit Status window, which is located under the Functions menu. For safety reasons, the liquid level of the individual reagent containers, as well as the capillary positions, should also be manually checked before each measurement and, if necessary, replaced or refilled. For detailed information, see “Refilling Containers Individually“. Cleaning the reagent containers when manually re-filling All reagent containers must be thoroughly cleaned at regular intervals and rinsed with distilled or de-ionized water. Impurities caused by dust or fluff must absolutely be avoided! The Trypan Blue is especially critical as it can become contaminated with microorganisms. In the case of such contamination, exact measurements are no longer possible. If the Trypan Blue solution is contaminated, intense areas may be visible in the image that will make image analysis difficult or even impossible. Replacing the reagents after 5 days is recommended. For detailed information, see “Refilling Containers Individually“. 3.2 E Cleaning Routines Carried out by the Liquid Management The Liquid Management plays a key role in the Cedex Analyzer. It is necessary to Prime the system at the beginning of the day, and to carry out an LM Shutdown prior to shut down of the system in the evening (see “Carrying out an LM Shutdown and HW Shutdown”). The Liquid Management automatically runs an Ultra Fast Clean routine after every sample measurement. During the Ultra Fast Clean (approx. 30 seconds), the entire Liquid Management system, including capillary tubes, flow chamber and sample port, are rinsed out thoroughly. Manual cleaning routines can be carried out in the Cleaning window. To open the Cleaning window, click on the Clean button in the Shortcuts area of the Control Center or select Cleaning routines in the Functions menu (see Figure 76). Figure 76: The Cleaning window of the analyzer 122 Cedex Analyzer Operator’s Guide Daily and Manual Maintenance and Cleaning Routines Cleaning Routines Carried out by the Liquid Management 3.2.1. Cleaning Options The following cleaning routines can be run manually: Fast Clean Standard Clean Intensive Clean Chamber Clean 1 Chamber Clean 2 Fast Clean and Standard Clean involve the entire Liquid Management system including capillary tubes, flow chamber and sample port. Therefore, always ensure that there is a Cedex Sample Cup attached to the sample port to prevent flooding. Fast Clean (with detergent, and distilled water for approx. 60 seconds) The entire Liquid Management system is rinsed with distilled water, then with detergent and finally with distilled water. Use this routine between measurements to remove dirt particles and air bubbles quickly from the flow chamber. Standard Clean (with cleaning solution, detergent, and distilled water for approx. 90 seconds) The entire Liquid Management system is rinsed with distilled water, cleaning solution, detergent and finally with distilled water again. This routine removes dirt particles and is used after measuring a set of samples or before a longer pause. Intensive Clean (with cleaning solution, detergent, and distilled water for approx. 20 minutes) The flow chamber is thoroughly rinsed with distilled water + cleaning solution + distilled water + detergent and finally distilled water. The detergent remains in the flow chamber for a longer period to work on resistant particles. The Intensive Clean routine is used on weekly basis to remove heavy and resistant contamination of the flow chamber, capillaries tubes, syringe and 8-way valve. Even the smallest dirt particle attached to the glass wall of the flow chamber can negatively influence a measurement. See also “Live View of the Flow Chamber”. If measurement values within a sample measurement show large variations, this could indicate that the flow chamber is soiled. E Intensive Clean with HCl A special Intensive Clean is required twice per month for a thorough cleaning. For this cleaning, a solution of 0.1 – 1 N HCl is used instead of detergent. Follow the instructions below: 1 Remove the Detergent container and replace it with an appropriate container with a 0.1 – 1 N HCl solution, taking care that the capillary tube reaches far enough into the solution. 2 Start Prime. 3 Start Intensive Clean after Prime has ended. 4 Replace the HCl container with the Detergent container at the end of the Intensive Clean process. 5 Start Prime again. 6 Start Standard Clean after Prime has ended. ■ Maintenance and Care 123 Daily and Manual Maintenance and Cleaning Routines Cleaning Routines Carried out by the Liquid Management The Chamber Clean 1 and Chamber Clean 2 cleaning routines are only required for the flow chamber. Chamber Clean 1 (with water for approx. 10 seconds) The flow chamber is rinsed at high pressure with distilled or de-ionized water being drawn in through the syringe. Use this routine to remove resistant protein aggregates, fluff particles or other obstructions from the flow chamber. Chamber Clean 2 (with water, detergent, and air for approx. 30 seconds) This routine is more intense than the Chamber Clean 1 procedure. Once the flow chamber is rinsed with water and detergent, the remaining liquid in the capillary tubes between the syringe and valve head is drawn through the flow chamber and then pressed back again with compressed air. Use this routine twice daily to remove resistant protein aggregates, fluff particles or other obstructions from the flow chamber. 3.2.2. The Hardware Management Window Prime and LM Shutdown can be executed in this window. An LM Shutdown must be carried out after the last measurement has been run and before shutting down the Cedex Software 2.2. The Liquid Management system is then prepared for an extended pause, i.e., overnight or weekend. An LM Shutdown is automatically preceded by a Standard Clean routine. The 8-way valve is then rinsed with distilled or de-ionized water to prevent crystallization, and compressed air finally presses the Trypan Blue solution back into its container (see “Carrying out an LM Shutdown and HW Shutdown”). 3.2.3. E Carrying out a Cleaning Routine The different cleaning routines always have the same starting procedure. Ensure that there is always a Cedex Sample Cup attached to the single sample port or placed in the DefaultCup position on the Multi Sample tray. Follow the instructions below: 1 Click on the Clean button in the Shortcuts area of the Control Center or else select Cleaning Routines in the Functions menu. The Cleaning window will open. 2 Click on the appropriate button (e.g., Fast Clean) to automatically start the cleaning routine. ■ The Cedex Analyzer is blocked during the cleaning routine, and the duration is continuously displayed in the Estimated Total Time field. 124 Cedex Analyzer Operator’s Guide Daily and Manual Maintenance and Cleaning Routines Live View of the Flow Chamber 3.2.4. Interrupting/Terminating a Cleaning Routine Use the EMERGENCY STOP button to interrupt the cleaning routine immediately if any leaks are detected in the Liquid Management system, even in the case of an Ultra Fast Clean being carried out automatically. The Intensive Clean procedure can be interrupted to shorten the long detergent phase in the flow chamber. Click on the Cancel button, which is only activated during the long detergent phase, in the Liquid Management window. 3.3 Live View of the Flow Chamber The Live View option can be activated by clicking on the appropriate check-box in the Cleaning window. This function allows for monitoring of the area in the flow chamber from which images are taken in order to check the effectiveness of a cleaning routine. In the Previous area, an image of the previous state of the flow chamber is displayed while the Current area on the right presents a live view of the flow chamber after a cleaning routine has been carried out. The Live View should be turned off while a measurement or cleaning routine is being carried out. If it has not been turned off, the Live View will be automatically stopped and the message, “warning: live view has been stopped automatically”, will appear in the message area of the Cedex Control Center. E Maintenance and Care 125 Automatic Adjustment 4 Automatic Adjustment The automatic adjustment adjusts the focus position to ensure that images of consistent quality are taken during measurements. The service technician will carry out a focus adjustment before the initial operation of the Cedex Analyzer. The focus adjustment is always necessary after the Analyzer has been moved. Additionally, Roche Diagnostics recommends running a focus adjustment once per month for control purposes. Both the brightness and the focus on the objects to be examined are optimally set during this focus adjustment. The focus adjustment lasts approximately 20 minutes and is done with the Cedex Calibration Beads included in the contents of delivery. If at all possible, the analyzer should never be turned off. If it is necessary to turn it off, the analyzer needs at least 2 hours to warm up before an Automatic Adjustment can be carried out. Proceed as follows to do the focus adjustment: 1 Open the Functions menu in the Control Center’s menu bar. 2 Click on Automatic adjustment to open the Automatic Adjustment and Alignment Verification window. 3 Pipette 1 ml of a well-mixed bead solution (Cedex Calibration Beads) into a Cedex Sample Cup. 4 Attach the Cedex Sample Cup to the sample port, or place the Cedex Sample Cup in the DefaultCup position on the Multi Sample tray (see “The Multi Sampler DefaultCup”). 5 Click on the Start Automatic Adjustment button. You will be asked to verify that the beads have been prepared. Click on OK to confirm and start the adjustment process. ■ E 126 Cedex Analyzer Operator’s Guide Automatic Adjustment Figure 77: The Automatic Focus Adjustment window after adjustment The automatic adjustment is automatically carried out in several steps. First, water is pumped into the flow chamber, after which the Cedex Calibration Beads are injected into the flow chamber. The complete path of the microscope stage is scanned as it moves to its lowest and then to its highest position. Based upon the obtained image information, a preliminary focus position is set. The area around the located focus position is then examined closely and scanned several times to find the optimal focus. An automatic cleaning of the flow chamber and the capillaries is done at the end of the adjustment. The focus adjustment’s time-progression is displayed as an estimated value in the form of a blue progression bar. The focus quality for every stage/focus position is displayed in a diagram. A distinct peak around the middle of the graph indicates the optimal focus position. The following criteria can be inspected to evaluate the result of an automatic focus adjustment: Verify that the pink line marking the newly set focus lies within close range of the distinct peak. E New and previous focus position values are both displayed in the message box appearing at the end of the focus adjustment. Ensure that variations between these values don’t exceed a range of +/-30. The image quality should be checked. A valid image shows clearly outlined beads with a bright cell interior. If any one or more of these criteria is not met, an authorized service technician must re-adjust the Cedex Analyzer. The Automatic Adjustment and Alignment Report can be printed out via the Print Report button. Maintenance and Care 127 Syringe Maintenance Removing the Syringe 5 Syringe Maintenance Moving parts of the Syringe Module may cause hand injuries. Never run a measurement on the Cedex Analyzer without the protective cover for the Syringe Module in place. When performing a syringe maintenance, be aware of the risks from moving parts. The flow chamber, tubes, syringe and 8-way valve are cleaned during the Intensive Clean routine carried out by the Liquid Management (see “Cleaning Options”). However, the syringe is subject to wear and tear and must, therefore, be regularly replaced to maximize the life span of the 8-way valve and to guarantee optimal performance. The syringe should be replaced approximately every 6 months under normal use of the analyzer. More frequent use may require more frequent changing of the syringe. To change the syringe, follow the steps specified in the sections below: 5.1 Removing the Syringe Follow the instructions below: E 1 Click on Syringe Maintenance in the Functions menu of the Control Center. The Syringe Maintenance window will open (see Figure 78). 2 Click on the Remove Syringe button. The syringe barrel will be moved to a position to allow easy removal. 3 Remove the protective cover. 4 Hold the syringe barrel by the Luer lock and turn it anti-clockwise to remove it from the 8-way valve (see Figure 79). 5 Once the connection is loosened, keep holding the syringe barrel in an upright position beneath the 8-way valve to prevent it from jamming with the plunger. 6 Remove the bottom screw that connects the plunger to the syringe module with the other hand. 7 Remove the syringe from the syringe module. ■ Figure 78: Syringe Maintenance window 128 Cedex Analyzer Operator’s Guide Syringe Maintenance Assembling and Installing the Syringe Luer Lock Syringe barrel Bottom screw connecting plunger to syringe module Figure 79: Syringe 5.2 Assembling and Installing the Syringe Rinse a new syringe with 70% alcohol and then with distilled or de-ionized water before installing it. Follow the instructions below: E 1 Gently press the plunger into the syringe barrel. 2 Insert the syringe back onto the syringe module. 3 Hold the syringe barrel by the Luer lock and turn it clockwise into the port of the 8-way valve. 4 Secure the plunger to the syringe module with the screw at the bottom. Ensure that the syringe barrel and plunger do not get jammed. 5 If the Syringe Maintenance window has not been opened yet, select Syringe Maintenance in the Functions menu on the Control Center. 6 Click on the Install button. The plunger will be correctly positioned and the syringe module initialized. 7 Ensure that there are no leaks in the Liquid Management system. This can be done with one of the cleaning routines in the Cleaning window. Interrupt the cleaning procedure immediately with the EMERGENCY STOP button if there are any leaks in the syringe module. 8 Put the protective cover back on. ■ Never use the Cedex Analyzer without the protective cover on the Multi Sampler and Syringe Module. Maintenance and Care 129 Syringe Maintenance Maintenance of the Syringe Guide and Spindle 5.3 Maintenance of the Syringe Guide and Spindle The syringe guide and spindle are mounted on either side of the syringe module inside the casing (see Figure 80). They should be lubricated half-yearly (or, when necessary, more often, e.g., if conspicuous noise comes from the syringe guide) with the lubricant supplied by your local Roche representative to guarantee optimal performance of the syringe. Follow the instructions below: 1 Remove the syringe (see “Removing the Syringe”). 2 Switch off the Cedex Analyzer. 3 Lubricate the top part of the syringe guide and spindle. 4 Switch on the Cedex Analyzer. 5 Click on Install in the Syringe Maintenance window. 6 Switch off the Cedex Analyzer. 7 Lubricate the bottom part of the syringe guide and spindle. 8 Switch on the Cedex Analyzer. 9 Click on Remove Syringe in the Syringe Maintenance window. 10 Install the syringe (see “Assembling and Installing the Syringe”). ■ E syringe guide spindle Figure 80: Syringe Guide and Spindle 130 Cedex Analyzer Operator’s Guide Maintenance of the Flow chamber, Microscope Optic, 8-Way Valve and the remaining Hardware Components 6 Maintenance of the Flow chamber, Microscope Optic, 8-Way Valve and the remaining Hardware Components To ensure that the Cedex Analyzer functions uninterruptedly, maintenance work is necessary at regular intervals. An arrangement for a maintenance contract with your local Roche representative is recommended. During maintenance, worn-out and defective components are replaced and the functioning of the Cedex Analyzer checked. Only an authorized service technician is permitted to carry out maintenance when the Cedex Analyzer needs to be opened! 7 Operational Data The Cedex System keeps track of some operational data including operating hours, number of measurements and liquid consumption. Select Operational Data in the Functions menu of the Cedex Control Center to open the Operational Data window. The values on the left-hand side of the window can be set to 0 by clicking on the Reset button. This can be useful for tracking the operational information for short periods of time. The values on the right-hand side track the overall operating hours, number of measurements and liquid consumption. These values cannot be reset. A report of the operational data can be printed out via the Print Report button. E Maintenance and Care 131 The System Suitability Test (SST) Creating SST Checkpoints 8 The System Suitability Test (SST) To ensure proper operation of the Cedex Analyzer and valid analysis results, it is essential that the system is in good condition. The majority of the critical parameters are regulated by design or preventive maintenance activities carried out by local Roche technical services. The routine check-ups performed by the user of the Cedex Analyzer mainly focuses on the liquid management process (such as flow chamber, capillaries etc.). A feature of the Cedex Software 2.2, the System Suitability Test (SST), is designed to help monitor the state of the system for quality supervision/assurance purposes. A routine check-up procedure that meets the system owner’s specific needs can be created using the SST software feature. Verification that the Analyzer is in the required condition comprises both manual checks (internal as well as external scrutiny of the equipment, e.g., chamber inspection) and various check-up and calibration measurements. These individual procedures are known as SST checkpoints. When an SST is set up on a Cedex System, checks and measurements will have to be performed on a regular basis. Passing the checkpoints will then be mandatory for normal continuation of measurement procedures. The System Suitability Test consists of different types of SST checkpoints. Each checkpoint needs to be created and its parameters, including the acceptance criteria, configured by an authorized user (the Superuser or Administrator). Once created and activated, the checkpoints apply to the whole system. 8.1 E Creating SST Checkpoints The System Suitability Test consists of different types of SST checkpoints. There are two main types of checkpoints: an SST requiring inspection or maintenance activity performed by the user (e.g., syringe change, chamber inspection) and SST procedures involving measurements with either Control Beads or Density Reference Standard Beads. In order to pass a checkpoint involving Control Beads measurements, the average result of a pre-defined number of one or more measurements needs to be valid according to the checkpoint criteria. A checkpoint requiring an inspection or maintenance activity demands an active confirmation in the System Suitability Test window that the activity or inspection has been performed. Each checkpoint needs to be created and its parameters, including the acceptance criteria, configured by an authorized user. For this, authorized users need to be assigned the SST edit function. Users who perform SST procedures only need access to the SST run function. Once created and activated, the checkpoints apply to the whole system. On some systems, an inactive list of proposed SST checkpoints may be automatically provided in the System Suitability Test List window. To activate these checkpoints, click in the box under the Active column for the checkpoint. A check mark will appear in the Active column, which indicates that the checkpoint has been activated. 132 Cedex Analyzer Operator’s Guide The System Suitability Test (SST) Creating SST Checkpoints 8.1.1. Creating SST Checkpoints With and Without Measurements To create a new SST-Checkpoint, proceed as follows: 1 Click on SST in the Functions menu to access the System Suitability Test List window, or else click directly on the SST button in the Control Center. 2 Click on the New button and the System Suitability Test New window will appear. Using this window, a measurement checkpoint or a manual checkpoint can be created. 3 To create a checkpoint for a manual check or maintenance activity, click on the SST Without Measurement button. This will open the System Suitability Test New window that allows for the creation of a checkpoint for a manual check. Enter an SST Name (e.g., Flow Chamber) and an SST Description that provides sufficient information for any user performing this SST. 4 To create checkpoints for calibration measurements, click on the SST including Measurement button. The appropriate System Suitability Test New area will appear. A set of parameters needs to be defined. See Table 2, for a detailed description of the parameters. 5 Click on the Save button to create a new SST checkpoint. The checkpoint will immediately be added to the System Suitability Test List. 6 Clicking on Close will close the window without creating an SST checkpoint. ■ Parameters for SST including Measurement: SST Name / SST Description Enter an SST Name and Description for identification purposes during routine check-up procedures. Overall Type Select the characteristic that is to be inspected during the measurements for this checkpoint (e.g., Total Cell Count, Total Concentration) from the drop-down list. Cell Type /Measurement precision / Sample Volume / Sample Initial Dilution Define different measurement parameters for different checkpoints to verify operational reliability in various situations. Target Value The Target Value serves as benchmark for the acceptance criteria. It can be based, for example, on the average result of a set of measurements carried out with Control Beads. Offset The offset in % determines the acceptance range applicable to the results of SST measurements carried out for this checkpoint based on the target value entered. Target Value Check / Upper Limit / Lower Limit If the Target Value Check is activated, the user carrying out SST measurements can enter another target value before running the first SST measurement for this checkpoint (e.g., when a new container of Control Beads is used). Acceptable limits for what can be entered by a user for the variable target value are set using Upper Limit and Lower Limit fields. E Note: the Upper Limit and Lower Limit fields are not related to the acceptable range for results from an SST measurement! The acceptable range for results is determined by the % entered in the Offset field. Fixed Target Value If the target value is not to be entered by users, the Fixed Target Value must be activated. Count For Passing Count for Passing refers to the number of SST measurements that has to be carried out for this checkpoint. Table 2: SST parameters for SST with Measurement Maintenance and Care 133 The System Suitability Test (SST) Creating SST Checkpoints In general, the Target Value is determined before the SST checkpoint is activated. For further information on the procedure for the determination of a target value Roche technical services provides appropriate recommendations. It is necessary to re-determine the target value if a new container of Control Beads is used. An SST checkpoint includes a validity period. This can be set in the System Suitability Test List in the Days Valid column. After this period of time, the SST procedures must be performed. If the SST procedure is not performed within the validity period, all measurements apart from SST measurements will be prohibited (e.g., the system status is changed to MeasurementLock). 8.1.2. Running a Water Blank Before an SST including Measurement can be run, a water blank (Water For Injection [WFI]) should be run to check the condition of the reagents. No more than 20 counts should be recorded for this measurement. This can be scheduled using the SST including Measurement button (see “Creating SST checkpoints with and without measurements”). The WFI measurement requires a relative deviation rather than an absolute deviation, which means that 0 cannot be used as a Target Value as a relative deviation from 0 will always be 0. Therefore, when setting up a WFI measurement, the Target Value should be set to 10 with a relative deviation of 100%. This will result in an acceptance range of 0 – 20 objects (see Table 2). 8.1.3. Setting up the SSTFailureReaction in the System Options Menu The reaction of the system to an SST failure depends on the configuration in the System Options. The System Options can be accessed under the Setup menu on the Control Center: E 1 Open the System Options and click on the General tab. 2 Look for the parameter SSTFailureReaction. Entering Restrict in the Value column will lead to prohibition of any further measurements, including SST measurements, in the event of an SST failure. This will require a manual unlocking of the system in the Lock – Unlock System area before measurement activity can be resumed (see “Locking – Unlocking the System”). If Warning is entered, measurement activity can be continued but there will be a warning about SST failure before a measurement is carried out. Choosing the Audit option will simply lead to a log entry in the audit trail file in the case of an SST failure. There will not be any restrictions or warnings. 3 Click on Save to store the change. ■ Measurements that are run despite the fact that not all SST procedures are up to date or valid will have no check-mark in the SST Valid box in the Measurement window. 134 Cedex Analyzer Operator’s Guide The System Suitability Test (SST) Performing an SST 8.2 Performing an SST All procedures related to the System Suitability Test can be controlled via the System Suitability Test List. To access the list, open the Functions menu in the Control Center and click on SST or directly click on the SST button in the Control Center. The System Suitability Test List provides an overview of all SST checkpoints and their current status. Valid SST checkpoints are displayed in black while red indicates an invalid checkpoint. SST checkpoints need to be carried out at regular intervals, the length of these intervals being specified in the Days Valid column. To confirm a checkpoint, either manual checks have to be done or measurements need to be carried out. It is recommended to include confirmation of checkpoints in the daily/weekly work routine and not to wait until the validity period of a checkpoint has expired. 8.2.1. Performing an SST with Measurements If the SST to be performed requires a measurement or series of measurements, do the following: 1 Select SST from the Functions menu on the Control Center. Alternatively, click on the SST button in the Shortcuts area of the Control Center. The System Suitability Test List window will appear. 2 Select the SST checkpoint to be confirmed by clicking on the 3 Click on Run SST to start the SST procedure. The System Suitability Test Measurement Run window will appear. The parameter settings can be viewed but not altered. 4 Whether or not the Target Value can be changed depends on configuration. If the Fixed Target Value option is not activated, the user will be able to change the target value. However, if the Target Value Check is activated, the user will have to enter a value within the defined limits (Upper Limit, Lower Limit). 5 Click on Run to start the SST measurement. The Measurement window will appear and the measurement will be carried out automatically. 6 Close the Measurement window. 7 Repeat measurement as often as required for this checkpoint (see note below). field to the left of the appropriate line. ■ E The Count For Passing value given in the System Suitability Test Measurement Run window indicates the number of measurements that have to be carried out for this checkpoint. The average value will be calculated from all of the measurements required for a particular SST checkpoint. The average value of all test measurements needs to be within the acceptance range. The acceptance range is defined by the target value and the offset (in %). In the event of an invalid SST measurement, the system will immediately be locked. Once in SSTLock, the system needs to be unlocked manually by authorized users before any further SST or other types of measurements can be carried out. If the average result of all test measurements for an SST checkpoint is valid, the checkpoint will automatically be displayed in black. Maintenance and Care 135 The System Suitability Test (SST) Tracking Trends in SST Results over Time 8.2.2. Performing an SST without Measurements For SST procedures that don’t require any measurements, clicking on the Run SST button will open the System Suitability Test Run window. The SST Name and/or Description should provide information regarding the nature of the manual check or the maintenance step that needs to be taken. Once the System Suitability Test Run window has been opened, do the following: 1 Perform the required inspection or maintenance routine. 2 Click on the Valid check-box in the middle of the System Suitability Test Run window if inspection or maintenance procedure was successful. 3 Add a comment in the Comment box (optional). 4 Click on the Save button to confirm the completion of the SST check and return to the System Suitability Test List window. ■ If the valid check-box has been activated, the checkpoint will automatically be displayed in black in the System Suitability Test List window. E Figure 81: System Suitability Test List window On some systems, an inactive list of proposed SST checkpoints may automatically be provided in the System Suitability Test List window. Check with the Administrator to see if these SST checkpoints should be activated. 8.3 Tracking Trends in SST Results over Time The results of SST checkpoints can be tracked over time using the SST Trending button. Trends for both checkpoints with and without measurements can be tracked. 8.3.1. Tracking Trends in SST Checkpoints with Measurements To see all of the results over time from a particular SST checkpoint with measurements, do the following: 1 Select the SST checkpoint to be monitored by clicking on the 2 Click on the SST Trending button to open the Trending list for SST with measurement window (see Figure 82). field to the left of the appropriate line. ■ 136 Cedex Analyzer Operator’s Guide The System Suitability Test (SST) Tracking Trends in SST Results over Time All of the measurements for the selected SST checkpoint are listed in this window. The Filter by area in the bottom left-hand corner can also be used to search for and list specific measurements based on date run and Reactor ID. The information in the Trending list for SST with measurement window can be exported via the Export button or printed via the Print button. The SST checkpoint results are displayed in the result column in the units of the Overall Type selected for that particularly SST checkpoint. Clicking on the normalized view checkbox will normalize the results to the target value and display the differences in percent. To create a chart showing result trends over time, do the following: 1 Click on the use checkbox to mark the measurements that should be included in the calculations for the trending chart. A indicates that the measurement will be used. All measurements will be included on the Trending Chart, but excluded measurements will be circled in red and not used for curve calculations. 2 Click on the Trending Chart button to create a Trending Chart. ■ Figure 82: Trending list for SST with measurement window Clicking on the Trending Chart button will open a Trending Chart window showing all of the SST measurements (marked  on the chart) (see Figure 83). If multiple measurements were required for a particular checkpoint, the average of the measurements is marked by , while the results from the individual measurements for that checkpoint are marked with an ×. E In addition, the following parameters are included: Target Value Upper limit Lower limit Invalid checkpoints (▲) Mean value Moving average Variation coefficient The Trending Chart can be enlarged or reduced (see “Enlarging the Histograms”), and can be printed out via the Trending chart print button. Maintenance and Care 137 The System Suitability Test (SST) Tracking Trends in SST Results over Time Figure 83: Trending Chart window There are several additional options in the Trending Chart window. Excluded measurements can be removed from the chart completely by clicking on the show excluded checkbox to remove the check mark. For SST checkpoints with multiple measurements, the individual measurements can be removed from the chart by removing the checkmark in the box next to single measurements, leaving only the average of the measurements. Clicking on the normalized view checkbox will normalize the results to the target value and display the differences in percent. Both the mean curve and the moving average curve can be shown or hidden by selecting or de-selecting the appropriate checkboxes. E 8.3.2. Tracking SST Checkpoints without Measurements To see results from SST checkpoints without measurements over time, do the following: 1 Select the SST checkpoint to be monitored by clicking on the highlight the whole line. field to the left of the appropriate line to 2 Click on the SST Trending button to open the Trending list for SST without measurement window (see Figure 84). All of the measurements for the selected SST checkpoint are listed in this window. ■ The Trending list for SST without measurement window shows all comments given for each SST check that was made and indicates whether the checkpoints passed or not. The list can be printed out via the Print button or exported in either a DIF or CSV-excel format via the Export button. Figure 84: Trending list for SST without measurement window 138 Cedex Analyzer Operator’s Guide The System Suitability Test (SST) Locking – Unlocking the System 8.4 Locking – Unlocking the System Measurements that are carried out after the validity period of an SST checkpoint has expired are marked as invalid in the Audit Trail. In addition, the system may be locked for any further routine measurements except SST measurements. The System Status describes the capability of the system for performing certain tasks involving the hardware. The current state of the system can be viewed in the Change System Status window, which is accessed by selecting the Lock – Unlock System option in the System menu of the Control Center (see Figure 85). The state of the system is set automatically depending on the validity of all SST checkpoints, and the configuration of the SSTFailureReaction parameter in the System Options. Depending on the configuration, if an SST checkpoint is out of date only SST measurements can be carried out. No routine measurements will be possible (Current State: MeasurementLock). Once all SST checkpoints are up to date and valid again, the system is fully usable and the Current State is automatically set to SystemOK. In the event of a failed SST procedure, the system may be locked for any further measurements including SST measurements (this is only the case if the SSTFailureReaction parameter in the System Options is set on Restrict (see “Setting up the SSTFailureReaction in the System Options menu”). The Current State will be automatically set to SSTLock. The system status can be changed manually by authorized users. Manually changing the system status may be necessary for a variety of reasons. For more details see the following table: Manually set Description of the manually set As a possible reaction to the following automatic System Status to: System Status: System Status: ManualLock Any action involving hardware is prohibited. SSTManualUnlock SST measurements (and any other process SSTLock after failed SST involving the hardware except routine procedure. measurements) are allowed. MeasurementManualUnlock System is fully usable but all measurements SSTLock, SSTManualUnlock are marked as “Invalid because of SST or MeasurementLock failure” in the Audit Trail. Warning System is fully usable but there will be a warning before a measurement is run, and the measurements will be marked “Invalid because of SST failure” in the Audit Trail. SystemOK System is fully usable until system rechecks SSTLock, SSTManualUnlock validity of SST checkpoints (which is done or MeasurementLock at an interval of 300 sec.). SSTLock, SSTManualUnlock or MeasurementLock E Table 3: Manually settable system status Maintenance and Care 139 The System Suitability Test (SST) Locking – Unlocking the System Figure 85: System Status window E 140 Cedex Analyzer Operator’s Guide Diagnosis of the Cedex Analyzer F Troubleshooting 1 Diagnosis of the Cedex Analyzer For technical support purposes, the user is able to run a diagnosis of the Cedex Analyzer at the request of an authorized service technician. The diagnosis of the System provides a file containing information about the system software and hardware. It contains a system description, hardware and software descriptions (i.e., product name, version), parameters and settings (i.e., focus position, white/black balance). To create the diagnosis file, follow the instructions below: 1 Click on the Setup menu on the Cedex Control Center. 2 Click on Diagnosis and the Diagnosis window will appear. 3 The hardware to be included in the diagnosis can be selected by checking the appropriate boxes in the Hardware to diagnose area or by checking the box beside Diagnose all hardware. The diagnosis of the system software is also optional and can be selected by checking the box beside Diagnose system software. 4 Click on Start Diagnosis to run the diagnosis of the Cedex Analyzer. 5 The diagnosis data can be saved by clicking on Save To File and printed by clicking on Print Data. ■ F Troubleshooting 141 Trace and Logging 2 Trace and Logging Trace and Logging are only required for support and problem detection purposes. Therefore, it is advisable to restrict access to Trace and Logging to the support team and users with extended permissions (e.g., the Superuser). Trace and Logging functionality should only be activated at the request of an authorized service technician. In order to avoid an exaggerated use of hard disk space, turn off the Trace and Logging functionalities as soon as the issue has been located and/or resolved. To activate or change Trace and Logging parameters, open the Setup menu in the Cedex Control Center. Clicking on Trace & Logging will open the corresponding window. The tracing functionality, as well as the logging functionality, can separately be enabled for individual modules of the Cedex Analyzer. Tracing is in the Off state by default. The application has two Trace Levels. The first one (tracing level Normal) is used for minimal tracing required for time critical problems. The second level (tracing level Extended) is necessary for a more detailed problem description. To set the Trace Level, click on the current status and a dropdown menu will appear from which level can be selected. Logging is in True state by default. Trace and log records are saved in files which are accessible by using Windows Explorer. The records are found in the C:\Cedex2 directory under CedexLog (CedexLogand_YYYY_MM_DD.log) and CedexTrace (CedexTrace_YYYY_MM_DD.log). Target files for tracing and logging data can be defined in the System Options menu. These files will automatically be created in the Cedex2 folder. The data will then be stored in the default target files as well as the newly defined target files. Open the Tracing (Logging) tab and enter the desired target file path for the TraceOutputPath (LogOutputPath) parameter in the Value column. 3 F The System Audit Trail File All user-initiated activities, as well as important actions carried out by the Cedex Software 2.2, are recorded in the Audit Trail file. The system also logs all errors in the audit trail, including information from the error message. For each activity the User, Measurement ID, Workarea Name, Reactor Identifier and Sample Identifier are given. The actions are classified by Event Types and a short message provides further explanation. To support monitoring of user-initiated activities, a search filter is available that also allows for defining the period of time which is to be searched. A report can be printed by clicking on Print Report. 142 Cedex Analyzer Operator’s Guide System Options und User Preferences G Appendix 1 System Options und User Preferences The following list provides a description of all of the Systems Options that can be found in the Cedex Software 2.2 via the Systems Options window found under the Setup menu of the Cedex Control Center. If an option exists in both the System Options window and the User Preferences window, the entries in the User Preferences window take precedence over the entries found in the System Options. For example, if the default Cell Type in the System Options window is “CT1”, but user “Joe” selected Cell Type “CT2” as the default in the User Preferences window when he was logged in the default Cell Type will be “CT2” when the user “Joe” is logged in. The defaults set in the System Options window will apply to new users who have not set their own defaults in User Preferences window. If the column SaveLastValue has been selected for a particular parameter (i.e., there is a cross in the column), any new value entered in the corresponding location will be automatically saved in the System Options or the User Preferences windows. For example, user “Joe” has set the default for the Cell Type in the Measurement section of his User Preferences window to “CT1” and has activated the SaveLastValue option. If “Joe” changes the Cell Type parameter to “CT2” when running a new measurement, “CT2” will be automatically saved as the new default in his User Preferences window and will be automatically recommended for the next measurement. The SaveLastValue function can be activated for all options in the System Options window and for all options in the User Preferences window for every individual user. If the system has been upgraded from some previous version to software version 2.2, it is possible that some default settings in the System Options may have slightly different values than those described in this manual. The settings described below apply to systems on which software version 2.2 has been installed as the original software. G Appendix 143 System Options und User Preferences Settings in the section “General“: Option Value Description ActualLanguage English Language used for the software Automatically StartHardware CellDistMin 1 2.0833 Save last value 1 = The Hardware Management is automatically started after the Cedex Server has been started and the first login into the software has been completed. Minimum cell distance [µm] for which cells are ascertained to be single cells with regard to the determination of the aggregate rate. Do not change this parameter without consulting with Roche technical services! CellDistRatio 1.3 Minimum relationship of the cell distance to the sum of the radii used for which cells are ascertained to be single cells with regard to the determination of the aggregate rate. Do not change this parameter without consulting with Roche technical services! CertificateStore G My Name of the certificate storage from which the certificate for the check of the license and the signature for the archive is searched. CleaningPort 0 Cleaning port (will not be used in the current version). Consumption HistoryRecord Count 25 The number of cleanings to be used for the estimation of the average time the cleaning will take. CriticalDiskSpace 1 The limit for the free memory space on the non-removable disk (in gigabyte). The user is warned when executing a measurement if the space is below this limit. DataBaseDrive MapName C: The drive on which the database is located (this will, for example, be used for checking the free disk space, see “CriticalDiskSpace“). DBDMOperator STDDBDM Operator Designation of the Dirt and Bubble Detection Operators. DefaultCupPosition 1 Cup Position for “DefaultCup” used for cleaning and maintenance routines in the Multi/Auto Sampler. DisableReagent Control 0 Disable reagent control (verification of reagent container levels). “0” means that the reagent control is active. DisplayedResult Types 12, 10, 9 ErrorLevelDisplay ToUser 3 FlowFactor 1.0 HistogramBarWidth 2 InnovatisCertificate Innovatis AG Test JpegQuality 95 Result types to be displayed in MultiRun window. Lowest level of error messages to be displayed to the user (1:only fatal, 2: also critical, 3: also errors, 4: all, including warning). Flow Factor, adjustable with the use of the Density Standard Reference Beads. The width of the histogram bars. Specification of the certificate to be used for inspection of the license. JPEG compression factor. Do not change this parameter without consulting with Roche technical services! 144 Cedex Analyzer Operator’s Guide × System Options und User Preferences Option MaxCellDensity Value 10000000 Description Save last value Maximum cell concentration (in cells/ml) per image. When this limit is exceeded, the user will be requested to dilute the sample. This warning will only directly appear as a warning box if the “ErrorLevelDisplayToUser” is set to “4”. MaxSedimentation Delay 2 Maximum acceptable delay (in seconds) between the end of the sedimentation phase and the beginning of the main scan in the case of the Cedex HiRes System. The user is warned if the time interval is exceeded. Measurement CriticalTime 90 Maximum acceptable time delay during a critical measurement phase (i.e., between the beginning of sample preparation to the capturing of the last image) when the measurement is interrupted with the Emergency Stop. If this time is exceeded, the results are not reliable (particularly the viability value) and the user is warned. MultiRunClear ListDateTime Date/time when the Multi Run list was cleared. × MultiRunClear ResultListDateTime Date/time when the Multi Run overall result list was cleared. × OverallTypeFor Exponential Regression ViableCell Density (not adjustable) Overall Type for the exponential regression used for the determination of doubling time and specific growth rate. Auto Sampler Default Sample Port used. Possible values for the Cedex Standard System: Auto Sampler/Single Port. SampleTraySize 20 Number of Cedex Sample Cups that the AS20 carousel or the MS20 Tray can hold. SchedulerTimer Period 5 Time interval (in seconds) in which the Scheduler should check its task list. SamplePortName SSTFailureReaction Restrict Reaction to a failed checkpoint. Possible values include Audit: only an entry in the Audit Trail, Warning: an additional warning before running a measurement, Restrict: the system is blocked. SSTTimerPeriod 300 Time interval (in seconds) in which the SST checkpoints are checked for validity. SSTTrending MovingAverage 3 SSTWorkarea standard Number of results used for the calculation of the “moving average” for the SST Trending Chart. G Default Workarea where the SST measurements are stored. StreamLiveImages 1 Use of “live image“ during cleaning routines in the Cedex Standard System(1=yes, 0=no). TrayTypeNumber 0 Sample Tray type used for the Multi Sampler. Appendix 145 System Options und User Preferences Settings in the section “Measurement“: Option Save last value 0 CellDiameter HistogramDividers (0) (0) (0) Divider settings for use in the cell diameter histogram. × CellType Std. Cells (V5.00) Default Cell Type for measurements. × Require to confirm the start of a multi run. CellTypeFocus Offset 0 Default focus offset for the creation of new Cell Types if the new Cell Type is not based on a previous Cell Type. CellType Sedimentation Duration 1 Default sedimentation time (in seconds) for the creation of new Cell Types if the new Cell Type is not based on a previous Cell Type. DefaultCombined Number 1 Number of images that should be added together for a summary of the measurements results in the “Measurement Statistics” histogram. Mask image required 0 Mask image required. Normal (or Medium, in the case of a system version update) Measurement PrescanRequired 1 ObjectDiameter HistogramDividers (0) (0) (0) Default precision for the measurement: minimum/normal/superior (or low/medium/high in the case of a system version update). × Use of the Prescan in the case of the Cedex HiRes System (0: don’t run, 1: run). Divider settings for use in the object diameter histogram. × Percentage value of images which must be valid to ensure the measurement is valid. × ReactorID Default ReactorID for measurements. × SampleID Default SampleID for measurements. × Default dilution factor for measurements. (1:2, 1:20 etc.). × Default sample volume for measurements (currently not adjustable). × PercentageOf ValidImages SampleInitial Dilution SampleVolume 146 Description AskBeforeMultiRun Measurement Precision G Value SuggestNext CupPosition 75.0 1:1 1000 1 Increase in cup position after every measurement, for example when running new measurements in the Measurement window. (only with Auto/Multi Samplers). Possible values: 0=don’t increase, 1=automatically increase. Workarea standard Cedex Analyzer Operator’s Guide Default Workarea for measurements. × System Options und User Preferences Settings in the section “Measurement List Default Filter“: Option Value Description Save last value CellType Measurement List Default Filter for CellType × DataSet Measurement List Default Filter for DataSet × Measurement List Default Filter for DataSet: Effective/Original/All × ProcessDateFrom Measurement List Default Filter for Process Date From × ProcessDateTo Measurement List Default Filter for Process Date To × ReactorID Measurement List Default Filter for ReactorID × Result types to be displayed in measurement list window × SampleDrawing DateFrom Measurement List Default Filter for Sample Drawing Date From × SampleDrawing DateTo Measurement List Default Filter for Sample Drawing Date To × SampleID Measurement List Default Filter for SampleID × Show result in measurement list window × Measurement List Default Filter for UserID × Measurement List Default Filter for Workarea × DataSetType ResultsTo ShowInList ShowResults Effective 12,10,9 0 User Workarea Standard Settings in the section “Hardware“: Option ChamberHeight Value 0.1 Description Save last value Height of the measurement chamber. Do not change this parameter without consulting with Roche technical services! ErrorLevelFor BatchStopping 1 Error level at which a Multi Run will be automatically interrupted. (1: only fatal, 2: also critical, 3: also error, 4: all, including warning) Multisampler Present 1 (not adjustable) Indication of whether an Auto/Multi Sampler is recognized. PixelsPermmX 480 (not adjustable) Number of pixels per millimeter in the x-axis of the images taken. PixelsPermmY 480 (not adjustable) Number of pixels per millimeter in the y-axis of the images taken. G Appendix 147 System Options und User Preferences Settings in the section “Data Exchange“: Option Value Description ArchiveCertificate Innovatis AG Archive Test Certificate that should be used for the designation and examination of archives for Archive/Restore. ArchiveFileMask {8} – {4} – {5} – {6} Archive filename mask (parameters {0} – {9} can be used). {0} date/time of archive start Save last value {1} date/time of measurement sample drawing time {2} date/time of measurement process time (i.e., from the original data set!) {3} measurement ID {4} workarea {5} reactorID {6} sampleID {7} userName (i.e., who processed the original data set!) {8} name of the Cedex System (i.e., the Cedex Serial Number) {9} description of the Cedex System ArchivePath AuditTrailExport FileName CTCExport FileName DataExchange StatusReport Interval AuditTrailExport CTCExport Default path that should be used for Archive/Restore. Default file name for the CSV export of Audit Trail entries. Default file name for exported CTC files. 3 Interval in seconds in which the progress bar is updated during Archive/Restore/Export/Import. ExportCertificate Innovatis AG Archive Test Certificate that should be used for the designation and examination of archives for Data Exchange (Export/ Import). ExportDelimiter ; ExportPath G C:\Cedex2\ archivetmp C:\Cedex2\ archivetmp ExportString Delimiter ” ImportPath C:\Cedex2\ archivetmp Default value separator for the CSV/Excel export of measurements. Default for the path that should be used for the Data Exchange export. Export file string delimiter. Default for the path that should be used for the Data Exchange import. Measurement ExportFileName Measurement Export.txt Default file name for CSV/Excel export of measurement results. SSTTrending ExportFileName SSTTrending Export Default file name for CSV/Excel export of SST Trending. Settings in the section “Tracing“: Option DeleteTraces OlderThan TraceOutputPath 148 Value 7 Description Number of days after which the tracefiles are deleted. C:\Cedex2\ Logs\ Default file name for the trace file. CedexTrace.txt Cedex Analyzer Operator’s Guide Save last value System Options und User Preferences Settings in the section “Logging“: Option DeleteLogs OlderThan LogOutputPath Value 30 C:\Cedex2\Logs\ CedexLog.log Description Save last value Number of days after which the logfiles are deleted. Default file name for the log file. Settings in the section “Series Default Filter“: Option Value DataSet effective Description Save last value CTC Series New Default Filter for DataSet × Measurement DateFrom CTC Series List Default Filter for Measurement Date From × Measurement DateTo CTC Series List Default Filter for Measurement Date To × ReactorID CTC Series List Default Filter for ReactorID × CTC Series List Default Filter for WorkArea × WorkArea standard Settings in the section “CTC Views Default Filter“: Option Value Description Save last value CreateDateFrom CTC Views Default Filter for Measurement Create Date From × CreateDateTo CTC Views Default Filter for Measurement Create Date To × ModifyDateFrom CTC Views Default Filter for Measurement Modify Date From × ModifyDateTo CTC Views Default Filter for Measurement Modify Date From × UserName CTC Views Default Filter for User name × ViewName CTC Views Default Filter for View name × Settings in the section “Audit Trail Default Filter“: Option Value Description Save last value Name Audit Trail Default Filter for Name × Surname Audit Trail Default Filter for Surname × UserName Audit Trail Default Filter for User name × Appendix G 149 System Options und User Preferences Settings in the section “Password Settings“: Option Value Description AttemptsToLogin 0 Maximum number of incorrect logins before the user is locked out. ExpiresInDays 30 Period of validity (in days) for passwords. MaxLength 50 Maximum password length. MinCharacters 1 Minimum number of letters a password must contain. MinDigits 0 Minimum number of numbers a password must contain. MinLength 1 Minimum password length. NeverExpires 1 Indication of whether passwords can become invalid (see also “ExpiresInDays“). Possible values: 0: passwords become invalid after “ExpiresInDays“ number of days, 1: passwords never become invalid. OldPassword ReusedAfter 0 Number of previously used passwords that cannot be re-used as new passwords. UseBlacklist 1 Use of Blacklist (passwords generally not allowed) Possible values: 0: don’t use, 1: use. WarningDays Before 3 Number of days in advance a user will be warned at login that a password is about to become invalid. Save last value Settings in the section “Reports“: Option Value Description ReportResultPath C:\Cedex2\ reporttmp Report result .xml path Report TemplatePath C:\Cedex2\ reporttmp The path to report templates (files extension *.lst) Save last value × Settings in the section “Focus Finder“: Option G 150 Value Description FocusFinder CoarseStepZ 10 (not adjustable) Increment for the rough scan during the focus adjustment. FocusFinder FineSamplesZ 20 (not adjustable) Number of measurement points for the fine scan during the focus adjustment. FocusFinder FineStepZ 2 (not adjustable) Increment for the fine scan during the focus adjustment. FocusFinderMaxZ 7000 (not adjustable) Maximum focus position increments for the focus adjustment. FocusFinderMinZ 2000 (not adjustable) Minimum focus position increments for the focus adjustment. SaveAutomatic AlignmentImages 1 Cedex Analyzer Operator’s Guide Determines whether the images should be stored with the automatic adjustment in the database (0: don’t save, 1: save). Save last value System Options und User Preferences Settings in the section “Report Settings“: Option Value Description Audit Trail Report Template standard The name of the report template for report type “Audit Trail” Automatic Alignment Adjustment Report Template standard The name of the report template for report type “Automatic Alignment Adjustment” CTCData Report Template standard The name of the report template for report type CTCData” Diagnosis Report Template standard The name of the report template for report type “Diagnosis” Multiple Measurement Report Template list The report template for multiple measurements Operational Data Report Template standard The name of the report template for report type “Operational Data” ReportLanguage English Single Measurement Report Template standard The default report template for single measurements SST Data Report Template standard The name of the report template for report type “SST Data” SST Trending Chart Report Template standard The name of the report template for report type “SST Trending Chart” SST Trending Data Report Template manual checkpoint list The name of the report template for report type “SST Trending Data” SST Trending Measurement Data Report Template measurement checkpoint list The name of the report template for report type “SST Trending Measurement Data” standard The name of the report template for report type “System Configuration” System Configuration Report Template Save last value Report Template Default Language G Appendix 151 System Options und User Preferences Settings in the section “External XML“: Option Value AppendTimestamp ToExternalXMLFile name 0 Append timestamp to external XML file name (0-False/1-True) AppendUsername ToExternalXMLFile name 0 Append user name to external XML file name (0-False/1-True) ExternalApplication C:\Cedex2\ ExternalXML DummyApp.exe ExternalApplication Callback 0 ExternalXML ExportPath C:\Export ExternalXML FileName CEDEX-XML Example.xml ExternalXML ImportPath C:\Import ExternalXML ReportLanguage Name English ExternalXML ReportTemplate Name list Magic Magic G 152 Description Cedex Analyzer Operator’s Guide The application providing external XML for Measurement input/output Call external application after external measurement processing (0-False/1-True) External XML output directory External XML file name External XML input directory External XML report’s language ID External XML report’s template name The application connection authentication string Save last value Index Index 8 8-Way Valve ...............................................................131 CTC View....................................................................... 86 Cultivation progress ................................................. 86 Cultivation Time Chart ............................................. 86 A Access Control ........................................................... 42 Access Rights ................................................. 102, 104 Administrator functions ........................................101 Administrator, operating system.......................... 25 Aggregate Histogram .............................................. 80 Aggregate Rate Value.............................................. 70 Aggregate Size ........................................................... 80 Alcohol ........................................................................120 Analysis parameters ..........................................55, 71 Analysis results .............................................76, 77, 79 Analysis software ............................................... 20, 22 Analyzer ................................................ 20, 49, 52, 119 ArchivePath ...............................................................117 Audit Trail ............................................................94, 142 AutomaticallyStartHardware ...............................107 Average Diameter ..................................................... 70 Avg Compactness ..................................................... 70 B BorderWidth ..............................................................116 Buffer ............................................................................. 51 C Calibration Beads ....................................................126 Capillary tube .............................................................. 56 Cedex Control Center .............................................. 22 Cell area ........................................................................ 84 Cell concentration .............................................. 19, 70 Cell Diameter Histogram ........................................ 82 Cell Type.....................................................55, 109, 112 creating ....................................................................111 deleting ....................................................................113 editing ......................................................................112 CFR 21, Part 11........................................................... 19 Chamber Clean 1.....................................................124 Chamber Clean 2........................................... 120, 124 Cleaning ......................................................................120 Cleaning routines .......................................... 121, 122 Cleaning solution ...............................................20, 51 Clear List button ........................................................ 62 Combine view ............................................................. 85 Compact Histogram ................................................. 84 Control Beads ...........................................................132 Control Center .....................................................43, 94 Control Unit ................................................................. 25 Copyrights .................................................................... 10 Count For Passing ......................................... 133, 135 Creating a Cultivation Time Chart ....................... 90 Cross-sectional area ..............................................115 CSV ................................................................................. 95 D Data analysis ............................................................... 22 Data Exchange ........................................................... 95 Data Management .................................................... 94 Data Selection Area ..........................................90, 91 Data Series .................................................................. 88 Data Sets ...................................................................... 76 Data Sets, editing ...................................................... 77 DeadAggregateApp ...............................................115 DeadAggregateMax ...............................................116 DeadAggregateMin ................................................116 DeadAppearance ....................................................115 Dead Cell Count ........................................................ 70 Dead cells’ aggregate appearance ...................115 Dead cells’ aggregate maximum .......................116 Dead cells’ aggregate minimum........................116 Dead cells’ appearance ........................................115 Dead cells’ size.........................................................115 Dead Conc. .................................................................. 70 DeadSize .....................................................................115 DefaultCup .................................................60, 107, 126 DefaultCup default position .................................. 60 DefaultCupPosition .................................................107 Default measurement parameters ...................... 99 Defaults ......................................................................... 99 Default Settings .......................................................109 Detergent .......................................................16, 20, 51 Diameter ................................................................56, 70 Diameter Histogram .......................................... 82, 83 Diameter Histogram sliders ................................... 83 Dilution factor ............................................................. 54 Dilution of cells ...................................................54, 56 Doubling Time ............................................................ 93 DSEffective .................................................................. 76 DSOriginal.................................................................... 76 E Effective......................................................................... 76 Emergency Stop......................................58, 125, 129 Enlarging the diagrams ........................................... 79 Error Level .................................................................... 65 Event window .......................................................43, 46 Excel ............................................................................... 95 Exclude images .......................................................... 74 Exponential Regression .......................................... 93 Export ............................................................................. 95 Export (Data Exchange) .......................................... 96 ExportPath .................................................................... 96 Export to file ................................................................ 95 Appendix G 153 Index Index F M Fast Clean...................................................................123 FCC Notification ........................................................ 15 Fit lowest common value button ......................... 92 Flow Chamber .........................................20, 131, 132 Focus adjustment ...................................................... 26 Focus position values ............................................127 Functions ...................................................................... 94 Functions menu ......................................................... 44 Functions, user .........................................................104 Maintenance ................................................... 119, 136 Maintenance check list .........................................120 Master Data menu .................................................... 45 Measurement................................................53, 58, 61 Measurement data ............................77, 86, 94, 106 MeasurementManualUnlock ..............................139 Measurement menu ................................................. 44 Measurement Offset ................................................ 92 Measurement parameters.................55, 62, 71, 77 Measurement procedure........................................ 21 Measurement Series Offset................................... 92 Measurement Statistics Histogram .................... 85 Menu bar ...................................................................... 43 Microcarriers............................................................... 16 Microscope Optic ....................................................131 Minimum pollution area .......................................116 MinPollutionArea.....................................................116 Multi Run ...............................................................44, 61 Multi Run Data Entry Window .............................. 61 Multi Sampler Measurement .......................................................... 62 Modifying Data Entry............................................ 65 Multi Sample Tray...............................................59, 61 G Graphical display ................................................69, 79 GUI.................................................................................. 22 H Hardware Management ...................44, 48, 67, 124 Help menu.................................................................... 46 HWM ................................................44, 46, 48, 67, 124 HW Shutdown ............................................................ 67 HW Startup .................................................................. 48 I Image ............................................................................. 72 Image, invalid ....................................................... 71, 74 Image View .................................................................. 73 Image View, individual............................................. 72 Import (Data Exchange) ......................................... 97 ImportPath ................................................................... 97 Incubation .............................................................21, 62 Intensive Clean ............................................... 120, 123 Interrupting .........................................................58, 125 Invalid image ............................................................... 74 L G 154 Lin ................................................................................... 93 Liquid Container Configuration ..................45, 108 Liquid Management ........................................20, 122 Live Operator ....................................20, 69, 109, 113 Live Operator parameters .......................... 113, 115 LivingAppearance ...................................................115 Living cells‘ appearance .......................................115 LM Shutdown .................................................... 67, 120 Location of the Analyzer ......................................... 26 Locking the System ................................................139 Lock Level ..................................................................108 Log .................................................................................. 93 Logging .......................................................................142 Logging In .................................................................... 47 Log Out.......................................................................... 68 LogOutputPath .........................................................142 Luer lock .....................................................................129 Cedex Analyzer Operator’s Guide O Object Diameter Histogram................................... 83 Offset.....................................................................92, 133 Operating mode ................................... 44, 54, 61, 62 Operational Data ....................................................... 94 Operator ......................................................................113 Overall Type ...............................................................133 P Parameters .....................................................55, 62, 77 Password ....................................................................100 Precision level ............................................................. 55 Prime ...................................................... 48, 53, 61, 120 Print .........................................................................93, 94 Processing parameters.......................55, 62, 71, 77 Production staff........................................................104 R Reagent containers .........................................50, 122 Reagent Kit .................................................................. 52 Reagent Kit Status .................................................... 44 Reagents....................................................................... 51 Refilling containers ................................................... 51 Replace Reagent Kit..........................................49, 52 Reports .................................................................94, 127 Reprocess..................................................................... 77 Research staff...........................................................104 Result Data area ..................................................57, 70 Result diagram ........................................................... 86 Index Index S V Sample ID..............................................................54, 57 Sample Port ..........................................................55, 56 Sample volume ....................................................54, 56 Save Last ...................................................................... 99 Scheduling .........................................44, 64, 120, 121 Securing Data ....................................................94, 117 Selection of Data Series ......................................... 88 Setup menu ................................................................. 45 Shortcuts area ............................................................ 46 Shutting down ............................................................ 68 Single sample port .................................................... 55 Single smple port ...................................................... 20 Specific Growth Rate ............................................... 93 Sphere ........................................................................... 84 Spindle.........................................................................130 SST ................................................................................132 SST edit .......................................................................132 SSTFailureReaction.................................................134 SSTLock ............................................................ 135, 139 SST run........................................................................132 Standard Clean .............................................. 120, 123 Starting the Software ............................................... 47 Std. Cells (V5.00) ....................................................... 55 Std. Dev. ........................................................................ 91 Syringe..................................................................52, 128 System functions ....................................................... 94 System menu .............................................................. 43 System options ........................................................... 45 System Options ........................................................107 System Options und User Preferences ...........143 System parameters ...................................45, 94, 107 System Suitability Test ...........................................132 Valid image .................................................................. 74 Validity .........................................................................135 Viability ................................................................... 21, 70 Viable Cell Count ....................................................... 70 Viable Conc.................................................................. 70 View mode ................................................................... 76 W Warn Level .................................................................108 Waste ......................................................................20, 51 Water .......................................................................20, 51 Workarea .......................................................... 100, 106 T Target Value ..................................................... 133, 135 Total Conc. ................................................................... 70 Total Object Count .................................................... 70 Trace .............................................................................142 TraceOutputPath ......................................................142 Trypan Blue ................................................. 20, 51, 122 Trypan Blue Exclusion Method ............................. 21 G U Ultra Fast Clean........................................................122 Unlocking the System ............................................139 Unlock Queue ............................................................. 58 User account .............................................................101 User groups ...............................................................103 User password..........................................................105 User preferences .....................................................109 User Preferences ....................................................... 98 User Role .......................................................... 102, 104 Appendix 155 Published by Roche Diagnostics GmbH Sandhofer Straße 116 68305 Mannheim Germany © 2011 Roche Diagnostics. All rights reserved. www.roche-applied-science.com 06412793001 0511 Performing a Single Measurement — (May 2011) Moving parts of the Multi Sampler may cause hand injuries. The Multi Sampler needle may cause injuries during operation. Never use the Cedex Analyzer without the protective cover in place for the Multi Sampler. Start the Cedex Analyzer and Software 1 Switch on the Cedex Standard Analyzer. 2 Switch on the monitor and PC. 3 Log in to Windows XP. 4 Start the Cedex Software 2.2 by double clicking on the Cedex Client icon located on the desktop (the Cedex Server should already be automatically started. It must be first started before the Cedex Software 2.2 can be started). The Log In window of the Cedex Standard Software 2.2 will open. 5 Enter the username in the User Name field and password in the Password field and press . The Cedex Control Center appears after a successful login. ■ 1 Click on the Measure button in the Cedex Control Center to open the Measurement window. 2 In the Measurement window, enter a clearly defined Reactor ID to describe the sample (e.g. the name of the cell culture or bioreactor name) in the Reactor ID area. You may either choose a Reactor ID from the drop down list or enter a new Reactor ID. 3 Enter a clearly defined Sample ID in the Sample ID area. Multiple Sample IDs can be listed under one Reactor ID. The Sample ID can be freely defined. 4 Choose the appropriate dilution factor from the Dilution drop-down list. For undiluted samples, a dilution factor of 1:1 should be entered. When a dilution of 1:2 is prepared, then 1 part cell suspension has been added to 1 part dilution medium. A dilution of 1:3 means that 1 part cell suspension has been added to 2 parts dilution medium. The dilution factor will be automatically taken into account in the calculation of the results. 5 Select the sample volume of 1000 µL in the Volume drop-down menu. 6 Enter comments (if desired) in the Comment box. 7 Select the sample port type in the Sample Port drop-down list: 䉴 Auto Sampler: for systems with a Multi Sampler. 䉴 Perform a Hardware Startup and Prime 1 Click on the HWM button in the Cedex Control Center to open the Hardware Management window. If the Hardware Management has not been started, the current status field will have the message “Not started”. 2 Click on HW Startup if the Hardware Management has not been started. The Hardware Management will start and the current status field will have the message “LM Shutdown”. 3 Ensure that a clean, empty Cedex Sample Cup is correctly positioned on the Multi Sample Tray in the DefaultCup position (usually sample cup position 1) or on the single sample port and click on Prime in the Hardware Management window. Single: for systems with a single sample port. 8 Enter the cup position for the sample in the Cup Position window if there is a Multi Sampler. 9 Select the cell type that optimally recognizes your cells from the Cell Type drop-down list: 䉴 Factory-installed cell type is Std. Size (V5.00) If a new cell type has been created, it can also be selected from the same Cell Type drop-down list. 䉴䉴䉴 ■ Cedex Standard Software 2.2.1 Quick Guide Carry out a Measurement For life science research only. Not for use in diagnostic procedures. 1/2 31550411 Cedex Standard Software 01-Quick Guide_May2011.indd 1 12.05.2011 15:24:17 Performing a Single Measurement — (May 2011) 10 Select the desired precision level in the Precision drop-down list: 䉴 Minimum: 10 images are used for the analysis. 䉴 Normal: 20 images are used for the analysis. 䉴 Superior: 30 images are used for the analysis. 11 Prepare the sample. The Cedex Standard Analyzer requires a volume of 1000 µL +/- 10%. Any greater variation in sample volume will lead to inaccurate results. 12 Attach the Cedex Sample Cup containing the sample to the sample port, or place it in the appropriate sample cup position on the Multi Sample Tray. The sample cup is correctly attached to the single sample port when it is in an upright position directly beneath it and the capillary tube almost reaches the base of the sample cup. 13 Click on the Start Measurement button to start the measurement. 14 When the measurement is finished, the top section of the Result Data area in the Measurement window will display the overall results from the measurement. The bottom section displays, in succession, the results from each image taken. 1 Open the Hardware Management window (HWM button on the Control Center). 2 Click on LM Shutdown to shut down the Liquid Management system. 3 To log out of the Cedex Control Center, click on Logout under the System menu or on the Logout button in the Cedex Control Center. The Cedex Software will be ended and the login window will reappear. 4 Alternatively, shut down the Cedex Software by selecting Exit under the System menu or by clicking on to close the Cedex Control Center window. 5 The security query, “Do you really want to exit the Cedex Control Center?“, will appear. Click on Yes to shut down the program. 6 The sample cup from the last measurement should remain attached to the sample port during the entire shutdown procedure and should only be removed when a new sample cup has been attached for the next measurement. In the case of a Multi Sampler, a sample cup should always be left in the DefaultCup position on the Multi Sample tray at all times (see Quick Guide “Working with the Multi Sampler”). ■ 05799902001��0511 ■ CEDEX and INNOVATIS are trademarks of Roche. Other brands or product names are trademarks of their respective holders. 31550411 Cedex Standard Software 01-Quick Guide_May2011.indd 2 Cedex Standard Software 2.2.1 Quick Guide Logging Out and/or Shutting Down For life science research only. Not for use in diagnostic procedures. 2/2 12.05.2011 15:24:18 Working with the Multi Sampler — (May 2011) Moving parts of the Multi Sampler may cause hand injuries. The Multi Sampler needle may cause injuries during operation. Never use the Cedex Analyzer without the protective cover in place for the Multi Sampler. Carrying out a Measurement with the Multi Sampler 1 Click on the Multi Run button on the Cedex Control Center to open the Multi Run window. 2 Fill 1000 µL +/- 10% of the samples to be measured into individual Cedex Sample Cups (maximum 20) and place them in the Multi Sample tray according to the desired sequence. Insert the tray into the Multi Sampler. 3 Click anywhere in the row of the MultiRun Measurements Preparation area that corresponds to the location of a cup containing a sample. The row will be converted to edit mode, and the sample and process parameters for the measurement can be defined. 4 Enter the sample data and parameter information as described in the section “Carry out a Measurement” in the Quick Guide “Performing a Single Measurement”. 5 Repeat steps 3 — 4 for the remaining samples to be measured. 6 Activate the status of each sample row by double clicking in the Status field of the row to be activated. The row appears pale blue, and further modifications of sample information is impossible. Return to the Edit status by double clicking on the Status area of the sample row to allow for further changes, if desired. 7 Alternatively, activate or deactivate all samples simultaneously by double clicking on the word Status in the column heading at the top of the Multi Run preparation area. Confirm the safety query with Yes to accept the modification. 8 After some or all rows have been activated, click on the Start button on the right-hand side of the Multi Run window to start the analysis of the activated measurements. The Multi Sampler DefaultCup The position of the Cedex Sample Cup used for Prime, LM Shutdown, calibration and cleaning routines is called the DefaultCup position. An empty Cedex Sample Cup must be manually placed in the position set for the DefaultCup before running LM Shutdown, focus adjustment, Prime and all cleaning routines. This Cedex Sample Cup does not differ from the usual sample cups. The standard (default) position for the DefaultCup is position 1 of the Multi Sample Tray. Using the Multi Sample Tray To insert the tray, gently push the tray into the notch until the automatic tray rope starts pulling it in. To eject the tray, gently push on the tray. The tray will be automatically ejected. The tray can only be ejected when the system is idle. It cannot be ejected if the system is moving or the needle is down in a cup. ■ For life science research only. Not for use in diagnostic procedures. 1/2 31550411 Cedex Standard Software 02-Quick Guide_May2011.indd 1 12.05.2011 15:24:49 Modifying Data Entry, Changing Samples Viewing results via the Multi Run Result List Information about the operation and process parameters for samples that have not yet been analyzed can be modified during the run as follows: At the bottom of the Multi Run window, the Analyzed Measurements field displays the list of results for measurements previously carried out. Measurements are listed in order of process time, from the newest measurements at the top of the list to the oldest measurements at the bottom. All measurements carried out using the Multi Run window will be displayed in this field unless the Clear Resultlist button has been pressed, which will clear all measurement results from the list. 1 Double-click on the Status field of the measurement to be modified. The status field will indicate that the sample is in edit mode. 2 Make desired changes to the measurement. 3 Double-click on the Status field to re-activate the measurement (status: active or scheduled). In addition, measurements displayed in this field can be restricted to only the measurements carried out by the user logged into the system (mine), measurements that have not yet been printed out (unprinted), and/or measurements carried out on that particular day (today). ■ Other results, such as Average Diameter, can be added for display in the result list via the User Preferences (see “Adjusting Result Display in the Measurement List and Multi Run windows” in the Operator’s Guide). Double-click on a measurement to view all results. If the result list has been cleared, previously carried out measurements can still be viewed, printed out and exported via the Measurement List window (see “Using the Measurement List” in the Operator’s Guide). Adding Measurements to the List while Measurements are Running 05799929001��0511 Sample rows in which data has not yet been entered can be filled out at any time while the Multi Run is running. In addition, sample rows containing finished measurements (status: done) can be cleared and prepared for a new measurement by double-clicking in the Status field of the row with the finished measurement. Sample data for a measurement cannot be modified after that measurement has begun. CEDEX and INNOVATIS are trademarks of Roche. Other brands or product names are trademarks of their respective holders. 31550411 Cedex Standard Software 02-Quick Guide_May2011.indd 2 Cedex Standard Software 2.2.1 Quick Guide Working with the Multi Sampler — (May 2011) For life science research only. Not for use in diagnostic procedures. 2/2 12.05.2011 15:24:49 Moving parts of the Multi Sampler may cause hand injuries. The Multi Sampler needle may cause injuries during operation. Never use the Cedex Analyzer without the protective cover in place for the Multi Sampler. Changing the Reagent Kit Refilling Individual Containers Proceed as follows to install or change the Reagent Kit: In order to ensure the optimal functioning of the analyzer, the reagent containers must be thoroughly cleaned before refilling with fresh reagents. Reagents can be refilled, or in the case of waste emptied, individually. 1 If the Liquid Management system has been primed, click on the HWM button in the Control Center to open the Hardware Management window. 2 Attach a clean Cedex Sample Cup to the sample port or place a sample cup in the DefaultCup position on the Multi Sample tray, and click on LM Shutdown in the Hardware Management window to shut down the Liquid Management. 1 Shut down the liquid management via the Hardware Management window as in step 1 — 2 of “Changing the Reagent Kit”, above. 2 Remove the reagent containers to be refilled, empty them and rinse thoroughly with distilled water. Empty waste container, if necessary. 3 Add fresh reagents to the appropriate reagent bottles and place them back in their correct positions on the reagent tray. 3 Remove the old Reagent Kit containers from the tray and dispose of the containers if necessary. 4 Place the new Reagent Kit containers in the appropriate positions on the Reagent Tray. 5 Insert the capillaries into the containers via the holes in the lids. Ensure that the capillary tubes are not bent and almost reach the base of the containers. 4 Insert the capillaries into the containers via the holes in the lids. Ensure that the capillary tubes are not bent and almost reach the base of the containers. 6 Select the Reagent Kit Status option in the Functions menu of the Cedex Control Center to open the Reagent Kit Status window. 5 Select the Reagent Kit Status option in the Functions menu of the Cedex Control Center to open the Reagent Kit Status window. 7 Click on the Replace all containers button in right-hand corner of the Reagent Kit Status window to confirm the changing of the Reagent Kit. The Reagent Control display at the bottom right-hand corner of the Cedex Control Center will turn from red to green and indicate the number of runs left. 6 Confirm the refilling of each reagent container individually by clicking on the respective Set Full button (or Empty button in the case of waste) in the Reagent Kit Status window. 8 ■ Attach a clean Cedex Sample Cup to the sample port or place a sample cup in the DefaultCup position on the Multi Sample tray, and perform a Prime via the Hardware Management window (HWM button on the Cedex Control Center). ■ Cedex Standard Software 2.2.1 Quick Guide Preparing and Maintaining the Analyzer — (May 2011) For life science research only. Not for use in diagnostic procedures. 1/2 31550411 Cedex Standard Software 03-Quick Guide_May2011.indd 1 12.05.2011 15:25:23 Cleaning the System Interrupting a Measurement Manual cleaning routines can be carried out in the Cleaning window. To open the Cleaning window, click on the Clean button in the Shortcuts area of the Control Center or select Cleaning routines in the Functions menu. An orange EMERGENCY STOP button is located on the left-hand side of the Measurement window and can be activated during the measuring procedure to interrupt the analysis process. If the EMERGENCY STOP is selected, an error message will appear asking, “Do you want to cancel the process?”. The following cleaning routines can be run manually: Fast Clean: Entire Liquid Management system is rinsed with detergent, and distilled water for approx. 60 seconds. 䉴 Standard Clean: Entire Liquid Management system is rinsed with disinfectant, detergent, and distilled water for approx. 90 seconds. 䉴 Intensive Clean: Entire Liquid Management system is rinsed with disinfectant, detergent, and distilled water for approx. 20 minutes. 䉴 Chamber Clean 1: Flow chamber is rinsed with water at high pressure for approx. 10 seconds. 䉴 Chamber Clean 2: Flow chamber is rinsed with water and detergent at high pressure for approx. 30 seconds. 䉴 Click on Yes to stop and abort the process immediately. If Yes is selected, the EMERGENCY STOP button will change to read Unlock Queue. The system must be unlocked by clicking on this button before more measurements can be run. 䉴 Click on No to put the process on hold until another action is chosen. If No is selected, the EMERGENCY STOP button will change to read Resume. Click on this button to resume the measurement process. Only use the Emergency Stop button in a case of emergency. Actual measurement data may be lost. 05799937001 ��0511 䉴 CEDEX and INNOVATIS are trademarks of Roche. Other brands or product names are trademarks of their respective holders. 31550411 Cedex Standard Software 03-Quick Guide_May2011.indd 2 Cedex Standard Software 2.2.1 Quick Guide Preparing and Maintaining the Analyzer — (May 2011) For life science research only. Not for use in diagnostic procedures. 2/2 12.05.2011 15:25:23

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