Transcript
Operating Manual MIRAX SCAN with Fluorescence Option Digitizer for Slides
Carl Zeiss
COPYRIGHT / TRADEMARKS
MIRAX SCAN
Prior knowledge of this manual is essential for proper MIRAX SCAN operation. You are therefore advised to familiarize yourself with its contents and, equally importantly, to follow special notes and instructions it contains regarding the safe product handling. We reserve the right to make changes as may be deemed appropriate in the interest of ongoing technical improvement. This manual is not subject to updating or revision services of any kind. ©
This document must not be forwarded to anyone, nor may its contents be duplicated, exploited or disseminated in any other way, unless express approval to do so has been procured. Failure to comply will create a liability for compensation of damages.
All rights are reserved in the event of a patent grant or registration of an industrial design. Any company or product name which is mentioned in this operating manual can be a trademark or a registered trademark. References to products of other manufacturers are provided for information only. They are not intended to express an approval or recommendation for use of such products. Carl Zeiss MicroImaging GmbH will not assume any liability as to the performance or the use of this type of products. The MIRAX SCAN has been developed, manufactured and licensed exclusively for Zeiss by 3DHISTECH Kft./Hungary.
Editor:
Carl Zeiss MicroImaging GmbH P.O.B. 4041, D - 37030 Göttingen Telephone: +49 (0) 551 5060 660 Fax: +49 (0) 551 5060 464 E-mail:
[email protected] www.zeiss.de
Operating manual no.: B 46-0125 e Date of issue:
2
September 1st, 2006
B 46-0125 e 09/06
MIRAX SCAN
TABLE OF CONTENTS
Carl Zeiss
TABLE OF CONTENTS Page 1
INTRODUCTION ..................................................................................................................5
1.1
Notes Regarding Operational Safety ......................................................................................5
1.2
Notes on Warranty................................................................................................................8
2
PRODUCT DESCRIPTION .....................................................................................................9
2.1
MIRAX SCAN General View...................................................................................................9
2.2
MIRAX SCAN Base Unit.......................................................................................................10
2.3
Product Designation and Intended Use ................................................................................11
2.4
Product Description and Main Features ...............................................................................11
2.5
Warning and Information Labels .........................................................................................12
2.6
MIRAX SCAN System Overview for Single Workplace Solution.............................................13
2.7
System Overview for Networking Solution ...........................................................................14
2.8
Objective Lens, Cameras and Adapter .................................................................................15
2.9
Accessory Components .......................................................................................................16
2.10
Power Supply and Lightsource.............................................................................................17
2.11
Fluorescence Option............................................................................................................17
2.12
Technical Data ....................................................................................................................18
3
START UP ..........................................................................................................................21
3.1
Initial Start Up .....................................................................................................................21
3.2
MIRAX SCAN Transportation...............................................................................................21
3.3 3.3.1 3.3.2 3.3.3 3.3.4 3.3.5 3.3.6
Terminal Ports and Operation Control Elements...................................................................22 Base unit.............................................................................................................................22 24 V power supply ..............................................................................................................22 Monitor ..............................................................................................................................22 Control Computer...............................................................................................................23 Sony DFW-X710 Fire Wire Camera ......................................................................................24 Cabling of Product Components .........................................................................................24
3.4
Connecting the X-Cite 120 Illuminator (Fluorescence Option) ..............................................24
3.5
Turning Power On...............................................................................................................25
3.6
Turning Power Off ..............................................................................................................25
4
OPERATION.......................................................................................................................26
4.1 4.1.1 4.1.2 4.1.3
Preparing Slides and Magazines ..........................................................................................26 Affixing Barcode Sticker to Slide..........................................................................................27 Inserting Slides into a Magazine ..........................................................................................28 Insertion and Removal of Magazines ...................................................................................29
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TABLE OF CONTENTS
MIRAX SCAN
5
SOFTWARE DESCRIPTION ................................................................................................ 30
5.1
Starting and Terminating the Scanning Software................................................................. 30
5.2 5.2.1 5.2.2 5.2.3 5.2.4 5.2.5 5.2.6 5.2.7 5.2.8
Brightfield Applications ....................................................................................................... 31 Digitizing Slides in Automatic Mode (Standard Procedure 1)................................................ 31 Preview Optimization in Manual Mode (Standard Procedure 2)............................................ 32 Digitization of Slides in Manual Mode (Standard Procedure 3) ............................................. 33 Brightfield scanning Automatic Mode ................................................................................. 34 Brightfield scanning Manual Mode...................................................................................... 43 Display Field for Live Image or Camera Image...................................................................... 52 Toolbar ............................................................................................................................... 54 Preview ............................................................................................................................... 55
5.3 5.3.1 5.3.2 5.3.3 5.3.4 5.3.5
Fluorescence Applications (Option)...................................................................................... 55 Scanning of Slides in Fluorescence scanning Manual Mode ................................................. 56 Scanning of Slides in Fluorescence scanning Automatic Mode ............................................. 57 Definition of Fluorescence Filters ......................................................................................... 58 Fluorescence Scanning Manual Mode.................................................................................. 59 Fluorescence Scanning Automatic Mode ............................................................................. 66
6
PREVENTIVE MAINTENANCE, TROUBLE SHOOTING AND SERVICE ............................... 69
6.1
Preventive Maintenance (Base unit) ..................................................................................... 69
6.2 6.2.1 6.2.2 6.2.3 6.2.4 6.2.5 6.2.6 6.2.7
Trouble Shooting ................................................................................................................ 70 Removing Protective Covers ................................................................................................ 72 Replacement of Fuses.......................................................................................................... 73 Replacement of Halogen Lamp............................................................................................ 74 Replacement of Lamp Module (for Fluorescence Option) ..................................................... 74 Removing a Slide................................................................................................................. 76 Removing a Magazine from the Transporting System .......................................................... 77 Installing and Removing the Filter Module (for Fluorescence Option) ................................... 78
6.3
Requesting Service .............................................................................................................. 79
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INTRODUCTION Notes Regarding Operational Safety
1
INTRODUCTION
1.1
Notes Regarding Operational Safety
Carl Zeiss
The MIRAX SCAN has been designed, manufactured and tested to comply with the standard requirements of DIN EN 61010-1 (IEC 61010-1) and IEC 61010-2-101, Safety Provisions Regarding Electric Measuring and Control Equipment, with due consideration of applicable requirements under Exhibit 1 of Directive 98/79/EC. Conformity with Directive 98/79/EC referenced above is documented by the MIRAX SCAN
-label.
This operating manual contains information and warnings of a kind that must be followed by owner/operator personnel. Warning and advisory notes which are used throughout this operating manual have meanings as follows: NOTE This symbol designates a note that should be closely followed. CAUTION This symbol alerts against a potential danger situation for the MIRAX SCAN. CAUTION This symbol alerts a potential danger situation for MIRAX SCAN users. CAUTION Beware of hot surfaces! CAUTION Emergence of laser radiation! CAUTION Detach power cord connector before any kind of intervention into the MIRAX SCAN! CAUTION There is danger of crushing or pinching!
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INTRODUCTION Notes Regarding Operational Safety
MIRAX SCAN
The MIRAX SCAN, including any of its original accessory components, should not be operated in any other way than described in section “Intended Use” of this operating manual. Any of the following notes should be strictly observed: In the event of any non-conforming type of use, including non-conforming use of assemblies or single parts, no liability will be assumed by the Manufacturer. This shall also apply to service or repair work of any kind, which is performed by other than duly authorized service personnel. All claims for warranty and warranty services will be null and void in any such case. Insert the power cord plugs only into a socket with a protective earth-ground contact. The MIRAX SCAN has a built-in protection function which must not be rendered ineffective by extension cables without protective (earth-ground) conductor. If protective devices are found to be ineffective, the MIRAX SCAN must be shut down and precautions must be taken to prevent unintended usage. For necessary repair work or work to restore proper operating condition, you should contact the Customer Service of Zeiss or Carl Zeiss Microscopy Operations. Electric power to the MIRAX SCAN is supplied via a special power supply It allows for operation at line voltages in the range of 100 V to 240 V ±10%, 50/60 Hz, without any extra facilities required for voltage transformation. Check that your local line voltage is compatible with MIRAX SCAN specifications before you turn power on. Remember to pull the power cord connector before you open the MIRAX SCAN or replace a fuse! Use only electric fuses which are rated for the specified nominal current. You are prohibited from using makeshift fuses or short-circuiting of a fuse holder. The MIRAX SCAN does not include any special facilities to protect from samples with an etching, potentially infectious, toxic, radioactive or other health-damaging effect. You are under obligation to comply with all currently binding legislation, notably, national accident prevention rules when handling samples of this kind. Dirt or dust may adversely impact the MIRAX SCAN’s operating capability. For this reason, measures must be taken to eliminate such influences to the maximum possible degree. During periods of non-use, the MIRAX SCAN must be protected with a dust cover. Check that power is turned off before you put the cover on. Refrain from physical contact with the lamp bulb. Pull the power supply plug and let the lamp cool down for an approximate time of fifteen minutes before you replace the lamp. During operation, there is potential danger of crushing or pinching your fingers in the area of magazine input or output stack motion. Please note that a running scan process must be interrupted before you can insert or remove a magazine.
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INTRODUCTION Notes Regarding Operational Safety
Carl Zeiss
Clogged or covered ventilation slots may result in a heat build-up with a damaging effect for the MIRAX SCAN. In extreme cases, this may also cause fire. Keep the ventilation slots always unobstructed and refrain from inserting or dropping objects into a ventilation slot. Do not use the horizontal stacker guide bar guard for raising, pulling or otherwise displacing of the MIRAX SCAN. A defective MIRAX SCAN does not classify as domestic waste. It must be properly disposed in accordance with currently valid legal requirements. The MIRAX SCAN may not be operated by other than duly instructed persons. Operating personnel must be fully aware of the potential dangers which a particular field of application involves. The MIRAX SCAN is a precision instrument which may suffer a significant reduction in operational functions or even physical destruction following intervention performed in any conconforming manner.
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INTRODUCTION Notes on Warranty
Carl Zeiss
1.2
MIRAX SCAN
Notes on Warranty
The Product Manufacturer warrants the MIRAX SCAN to be free from faults in material and workmanship at the moment of passing into the user’s ownership. Defects must be notified immediately on identification and maximum efforts must be undertaken in order to the amount of damage as small as possible. On receiving notice of a fault, the Product Manufacturer will be under obligation to remove the fault, at his own option, either by providing adequate repair services or by delivering a faultless product for replacement. No warranty will be accepted in cases of natural wear (notably, wear and tear parts) or improper product handling. The Product Manufacturer will refuse any liability in the event of damage resulting from faulty operation, negligence or unauthorized intervention into the product, notably, from the replacement of product parts or the usage of accessory parts from other manufacturers. Any such case will void the user’s claim for warranty. Except for action which is explicitly described in this operating manual, you are prohibited from performing any kind of maintenance or repair work on the MIRAX SCAN. Only Zeiss Customer Service personnel or specifically authorized representatives are allowed to handle repair work. On identifying a situation of malfunction, you should, first of all, contact the appropriate Carl Zeiss Representative Office.
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PRODUCT DESCRIPTION MIRAX SCAN General View
2
PRODUCT DESCRIPTION
2.1
MIRAX SCAN General View
1 2 3 4 5 6 7 8
Carl Zeiss
24 V power supply) 30" TFT monitor Mouse Image Analysis XEON workstation Keyboard MIRAX SCAN base unit Slide magazine with cover X-Cite fiber-coupled illuminator (option)
Fig. 2-1
MIRAX SCAN general view
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PRODUCT DESCRIPTION MIRAX SCAN Base Unit
Carl Zeiss
2.2
1 2 3 4 5 6 7 8
MIRAX SCAN Base Unit
Protective cover of scanner Magazine output stack Magazine input stack Protective cover for magazine loader Safety rails Sony DFW-X710 scan camera X-Cite fiber-coupled illuminator (option) X-Cite illumination adapter (option)
Fig. 2-2
10
MIRAX SCAN
MIRAX SCAN base unit
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2.3
PRODUCT DESCRIPTION Product Designation and Intended Use
Carl Zeiss
Product Designation and Intended Use
Manufacturer’s designation: MIRAX SCAN The MIRAX SCAN is intended for digitization of biological specimens and samples of human or animal bodies on smooth slides in transmitted light mode and reflected light fluorescence mode (optionally available). Typical applications are (but not limited to): − Hospitals − Medical practices − Universities and colleges − Industry
2.4
Product Description and Main Features
Essential performance features of the MIRAX SCAN are: − Robust and stable mechanical base unit − Intuitive operation control via keyboard and mouse − Maximum fill capacity of 50 slides per magazine − HAL 12 V, 5 W illuminator for transmitted light operation − Reflected light fluorescence option − Optional Optovars for flexible, user-selected adaptation of magnification scale − High-resolution scanner imaging optics − Max. scanner fill capacity for six magazines − Automatic feeding and output of slides − Automatic identification of slides through barcode detection − Automatic sample recognition and digitization of sample detected on slide
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Carl Zeiss
2.5
PRODUCT DESCRIPTION Warning and Information Labels
MIRAX SCAN
Warning and Information Labels
Carl Zeiss
Fig. 2-3
12
Warning and information lebals
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2.6
PRODUCT DESCRIPTION MIRAX SCAN System Overview for Single Workplace Solution
Carl Zeiss
MIRAX SCAN System Overview for Single Workplace Solution
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Carl Zeiss
2.7
14
PRODUCT DESCRIPTION System Overview for Networking Solution
MIRAX SCAN
System Overview for Networking Solution
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2.8
PRODUCT DESCRIPTION Objective Lens, Cameras and Adapter
Carl Zeiss
Objective Lens, Cameras and Adapter
View/Drawing
Description and technical specifications In standard delivery version, the MIRAX SCAN is configured with a 20x / 0.8 Plan-Apochromat objective.
40x /0.95 Corr Plan-Apochromat objective (optionally available)
Sony DFW-X710 Fire Wire
Without illustration
Preview camera with LED backlight illuminator and reflected light illumination
Without illustration
The MIRAX SCAN comes with a C-mount adapter 1x in standard delivery version.
Without illustration
C-mount adapter 0.63x (optional)
Without illustration
Optovar 1.25x P&C (optional, for transmitted light only and only for combined use with optional fluorescence kit)
Without illustration
Optovar 1.6x P&C (optional, for transmitted light only and only for combined use with optional fluorescence kit)
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PRODUCT DESCRIPTION Accessory Components
Carl Zeiss
2.9
MIRAX SCAN
Accessory Components
Graphical view
Without illustration
Description and technical specifications
Ordering code
Magazine Maximum capacity for 50 slides, with protective cover for safe storage of slides
415000-0100-000
Slide Magazine Universal with metal bottom Maximum capacity for 50 slides, with protective cover for safe storage of slides
415000-0102-000
Barcode stickers
415000-0101-000
The MIRAX SCAN may not be operated with other than original magazines.
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PRODUCT DESCRIPTION Power Supply and Lightsource
MIRAX SCAN
2.10
Carl Zeiss
Power Supply and Lightsource
Graphical view
Description and technical specifications
Ordering code
24 V power supply
-
HAL 12 V, 5 W 000000-0467-436 for standard configuration, transmitted-light mode
2.11
Fluorescence Option
Graphical view
Description and technical specifications
Ordering code
Without illustration
Fluorescence unit for MIRAX SCAN base unit
415001-9901-000
Without illustration
X-Cite 120 FL illumination system/iris with light guide of 3 m length
000000-1313-180
Without illustration
X-Cite 120 lamp module, spare
000000-1313-162
Without illustration
X-Cite 120 illuminator adapter, 35 mm
000000-1313-161
Without illustration
FL P&C reflector module
424920-0000-000
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PRODUCT DESCRIPTION Technical Data
Carl Zeiss
2.12
MIRAX SCAN
Technical Data
Phys. dimensions (width x depth x height) MIRAX SCAN base unit................................................................... approx. 740 mm x 580 mm x 450 mm Control computer........................................................................... approx. 206 mm x 560 mm x 440 mm Monitor (19”)................................................................................. approx. 420 mm x 240 mm x 490 mm Power supply.................................................................................. approx. 170 mm x 300 mm x 110 mm Weight details MIRAX SCAN base unit.........................................................................................................approx. 26 kg MIRAX SCAN base unit with fluorescence option..................................................................approx. 29 kg 24 V power supply .................................................................................................................approx. 2 kg Ambient conditions Transportation/shipment (packed) Permissible ambient temperature .....................................................................................-40 °C to +70 °C Storage Permissible ambient temperature ....................................................................................+10 °C to +40 °C Max. allowed relative air humidity (non-condensing)............................................................75 % at 35 °C Operation Permissible ambient temperature ....................................................................................+10 °C to +40 °C Max. permissible relative air humidity.................................................................................. 75 % at 35 °C Max. height level of operation site ................................................................................................ 2000 m Air pressure ...............................................................................................................500 hPa to 1060 hPa Degree of pollution ................................................................................................................................. 2 Operating data Category of operating environment ........................................................................... closed room facilities Protection class......................................................................................................................................... I Internal protection degree ................................................................................................................. IP 20 Electrical safety ............................................................... under DIN EN 61010-1 (IEC 61010-1) and taking CSA and UL regulations into account Over-voltage category ............................................................................................................................. II Radio interference suppression ..............................................................................under EN 55011 class B Noise immunity ......................................................................................................... under DIN EN 61326 Base unit line input voltage.................................................................................................... 24 V DC ±1 V
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PRODUCT DESCRIPTION Technical Data
Carl Zeiss
24 V power supply Category of operating environment ...........................................................................closed room facilities Protection class......................................................................................................................................... I Internal protection degree ................................................................................................................. IP 20 Line input voltage ...................................................................................................100 V AC to 240 V AC Line input frequency ................................................................................................................... 50 / 60 Hz Max. power consumption .................................................................................................................50 VA Secondary voltage .........................................................................................................................24 V DC Max. secondary current ........................................................................................................................ 3 A Fusing...................................................................................................... 2 x T 2.5 A / H, 250 V, 5 x 20 mm Lightsources Halogen lamp (transmitted light operation):.........................................................................HAL 12 V, 5 W Average lifetime performance of halogen lamp (000000-0467-436) ...................................... 4000 h Lamp module for X-Cite 120 (for fluorescence option)........................................................... 85 V, 120 W Halogen high-pressure metal-vapor short-arc lamp Average lifetime performance of lamp module (000000-1313-162)....................................... 1500 h Software MIRAX SCAN operation control ................................................... included in MIRAX SCAN delivery scope MIRAX Viewer fluorescence module (optional).............................................................. 415010-0112-000 MIRAX Viewer (optional)............................................................................................... 415010-0103-000 MIRAX Viewer TMA module (optional).......................................................................... 415010-0107-000 3D MIRAX Viewer module (optional)............................................................................. 415010-0102-000 MIRAX Viewer module teleconsultation server (optional)............................................... 415010-0108-000 MIRAX SCAN standard configuration Objective lens .................................................................................................. Plan-Apochromat 20x / 0.8 Magazines ............................................................................................................... 6 standard magazines ........................................................................................................................1 Slide Magazine Universal Camera ............................................................................................................. Sony DFW-X710 Fire Wire Camera adapter..........................................................................................................C-mount adapter1x Identification of slides: Slides are identified by preview camera.................................................. Barcode area is saved as a picture Barcode label is interpreted as a character string, with capability for interpretation of the following types of 1D and 2D barcodes: BC412 (Standard encoding type); Codabar (Standard encoding type); Code39 (ASCII encoding); Code93 (ASCII encoding); Code128 (UCC/EAN128) (ASCII encoding); DataMatrix (Numeric encoding, Alpha encoding, AlphaNumericPunc encoding, AlphaNumeric encoding, ASCII encoding, IS08 encoding); EAN8 (Numeric encoding); EAN13 (Numeric encoding); Interleaved 2/5 (Numeric encoding); Maxicode (Encoding mode 2, 3, 4, 5, 6); MicroPDF417 (Standard encoding type); PDF417 (Standard encoding type); Pharma (Numeric encoding); Planet (Numeric encoding); Postnet (Numeric encoding); QR (QR code Model 1, 2 encoding); RSS (RSS 14, RSS 14 Stacked, RSS 14 Stacked Omni, RSS 14 Truncated, RSS Expanded, RSS Expanded Stacked; RSS Limited encoding); UPC-A (Numeric encoding); UPC-E (Numeric encoding)
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PRODUCT DESCRIPTION Technical Data
MIRAX SCAN
Slide specifications Standard magazines: Phys. dimensions: .................................(25.6 to 26.8) mm x (75.0 to 76.2) mm; (0.9 to 1.2) mm thickness ..................................................................................................45° beveled corners and grounded edges .................................................................................................................................colored barcode area Slide Magazine Unisversal (415000-0102-000): Physical dimensions: ............................. (24.6 to 26.0) mm x (75.0 to 76.2) mm; (0.9 to 1.2) mm thickness .................................................................................................................................colored barcode area Image digitization 1/3" type progressive SCAN IT CCD Pixel size...................................................................................................................... 4.65 µm x 4.65 µm Pixel resolution with 20x objective and C-mount adapter 1x ......................................................... 0.23 µm Control computer and required system resources CPU..................................................................................................................................2 x Intel 2.6 GHz RAM...................................................................................................................................................2 GB Harddrive .......................................................................................................................................130 GB Communication ports .............................................................................................................2 x Fire Wire ............................................................................................................................................... 1 x USB 2.0 .............................................................................................................................................. GB Ethernet Keyboard................................................................................................................................................... Mouse.......................................................................................................................................................
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3
START UP
3.1
Initial Start Up
START UP Initial Start Up
Carl Zeiss
The base unit is shipped in a commercial polyethylene container with outer carton packaging as is customary in the trade. This base unit set includes magazines, slides, barcode stickers, replacement lamps, a dust-protection enclosure and tooling. The control computer and monitor come in separate outer carton packages! The MIRAX SCAN classifies as a product requiring installation by Manufacturer personnel! For a properly operation of MIRAX SCAN, installation and initial start up must be performed by Zeiss Service technicians. You should dispose of original packing parts in accordance with local regulations or keep them for later storage or reshipment of the product to the Manufacturer.
3.2
MIRAX SCAN Transportation
Fig. 3-1
MIRAX SCAN transporting handles
Do not use the blue horizontal stacker guide bar guard (3-1/1) to raise, shift or transport the product. For transportation, four carrying handles (3-1/2) are provided at the bottom plate of the basic MIRAX SCAN unit. • Turn power to the MIRAX SCAN and its peripherals off and detach all cables to external instruments. • Pull carrying handles out (3-1/2) until mechanical stop position (3-1/B). • Turn carrying handles by 90° (3-1/C). • The MIRAX SCAN can now be safely transported by two persons. • Once the MIRAX SCAN is at the designated installation site, the carrying handles (3-1/A) can be
pushed back into idle position.
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Carl Zeiss
START UP Terminal Ports and Operation Control Elements
MIRAX SCAN
3.3
Terminal Ports and Operation Control Elements
3.3.1
Base unit
The connector back panel provides the terminal points for the power supply cord (+24 V DC) (3-2/1) to link the unit with the 24 V power supply, a ready-for-operation LED indicator (3-2/2) and a port for the trigger cable (3-2/3) for scan camera operation.
Fig. 3-2
Terminals at base unit
The MIRAX SCAN further provides a terminal for computer connection of the MIRAX SCAN via USB control cable (3-2/4) and a Fire Wire terminal for connection of the preview camera (3-2/5) with the control computer.
3.3.2
24 V power supply
The power supply is designed to supply the base unit with direct voltage of 24 V. Located at its front is the main power switch (3-3/1). Its back panel contains the line power inlet (3-3/3) with integrated fuse section and the nondetachable power cord (3-3/2) for power supply to the base unit.
3.3.3 Fig. 3-3
22
Terminals at 24 V power supply
Monitor
For the various types and locations of operation control elements at the monitor, you should refer to the special user manual which is included in MIRAX SCAN delivery.
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3.3.4
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
START UP Terminal Ports and Operation Control Elements
Carl Zeiss
Control Computer
Fire Wire jack terminal DVD drive (RW) DVD drive 3.5“ diskette drive On/off switch Two USB jack terminals Line power inlet Keyboard terminal Mouse terminal Four USB jack terminals – for connection with the basic MIRAX SCAN unit Fire Wire jack terminal – for connection with the scan camera Network jack terminal DVI terminal – for connection with the monitor DVI terminal Fire Wire jack terminal (separate plug-in card: 410358-0000-000) – for connection with preview camera
Fig. 3-4
Terminal points and operation control elements of control computer
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Carl Zeiss
START UP Connecting the X-Cite 120 Illuminator (Fluorescence Option)
3.3.5
MIRAX SCAN
Sony DFW-X710 Fire Wire Camera
A Sony DFW-X710 Fire Wire is used as the scan camera. The terminal for trigger cable connection (3-5/1) and the video output port (3-5/2) Fire Wire (IEEE 1394/iLink) are located on the back of the camera.
3.3.6
Fig. 3-5
Terminals at Sony camera
Cabling of Product Components
For required cable connections, the supplied cables must be plugged as shown in Fig. 3-2, Fig. 3-3, Fig. 3-4 and Fig. 3-5. All cable connections must be checked for firm seating. A defective cable must not be connected. It must be replaced with a cable found to be in proper operating condition. Contact the Zeiss Service for support in such cases.
3.4
Fig. 3-6
Terminals of X-Cite 120 illuminator
Connecting the X-Cite 120 Illuminator (Fluorescence Option)
The fiber-coupled X-Cite 120 illuminator outputs the light that is required for excitation in fluorescence mode. Line power is supplied on the back of the illuminator (3-6/1). Connection between the X-Cite illuminator and the MIRAX SCAN is maintained via a light guide. One end of the optical fiber (3-6/2) must be plugged into terminal (3-6/3) of the illuminator, the other end (3-7/3) into the illumination adapter (3-7/2) on the back of the MRAX SCAN. This end must be additional fixed with a knurled screw (3-7/4). Use clamping screw (3-7/1) at the connector flange of the MIRAX SCAN to fix the collimator (3-7/5) of the illumination adapter.
Fig. 3-7
24
Illumination adapter at the back
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3.5
START UP Turning Power On
Carl Zeiss
Turning Power On
To transfer all components to power-on state, the 24 V power supply, the control computer and the monitor must be turned on individually. • Begin by turning power to the 24 V power
supply on. Use the main power switch (3-3/1) for this purpose. • Press the main power switch on the computer
(3-4/5) to turn on power to the control computer. The operating system will start. • Turn power to the monitor on. • For working in fluorescence mode (option), turn
X-Cite illuminator on with power switch (3-8/2) and use setting wheel (3-8/1) to adjust for maximum illumination intensity.
Fig. 3-8
Turning the X-Cite 120 illuminator on and off
• Wait twenty minutes until the lamp has reached
its nominal brightness! The MIRAX SCAN is ready for operation.
3.6
Turning Power Off
• Exit MIRAX software. • Shut down computer as required by Windows routine rules. • Turn 24 V power supply off, using the main power switch (3-3/1). • Turn monitor off. • Turn X-Cite illuminator (3-8/2) off, using the main power switch (only for fluorescence mode).
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OPERATION Preparing Slides and Magazines
Carl Zeiss
4
OPERATION
4.1
Preparing Slides and Magazines
MIRAX SCAN
You may use any type of slides and cover slips that meet the following specifications: For standard magazines: Slides
Cover slips
Length:
75.0 to 76.2 mm
Max. length:
50 mm
Width:
25.6 to 26.8 mm
Max. width:
22 mm
Thickness:
0.9 to 1.2 mm
Thickness:
No. 1 and 1.5 (0.13 to 0.16 mm and 0.16 to 0.19 mm, respectively)
–
45° beveled corners
–
Grounded edges
–
Colored area for placement of barcode stickers
The horizontal standoff between the slide edges and those of the mounted cover slip should be 1 mm to 2 mm. The edges of slide and cover slip must be parallel with each other. Please check that no part of a cover slip protrudes from any of the slide’s edges when mounting the cover slip onto the slide. For Slide Magazine Universal (magazines with metal bottom) (415000-0102-000): Slides
Cover slips
Length:
75.0 to 76.2 mm
Max. length:
50 mm
Width:
24.6 to 26.0 mm
Max. width:
24 mm
Thickness:
0.9 to 1.2 mm
Thickness:
No. 1 and 1.5 (0.13 to 0.16 mm and 0.16 to 0.19 mm, respectively)
–
Colored area for placement of barcode stickers
As can be seen from these specifications, metal bottom magazines accept any type of slide which is produced in accordance with ISO 8037/1 international standard requirements. Besides, all slides with features as specified for use with standard magazines will also fit this type of magazine. The edges of a slide and its cover slip should be mutually parallel. Please check that no part of a cover slip protrudes from any of the slide’s edges when mounting the cover slip onto the slide. Please note that MIRAX SCAN slide handling procedures may provide reduced reliability if not grounded slides are used.
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MIRAX SCAN
4.1.1
OPERATION Preparing Slides and Magazines
Carl Zeiss
Affixing Barcode Sticker to Slide
A slide’s barcode area (4-1/3) is recorded by the preview camera and displayed by software. Make sure that a marginal stripe of 1 to 2 mm remains on all sides between the sticker label and the barcode area outer limits. • Strip off a barcode label from the barcode roll
and affix it as shown in Fig. 4-1 to the colored area (4-1/3) so it sticks flat (wrinkle-free). • Note that a barcode (4-1/4) must be affixed on
the specimen side (with cover slip) (4-1/2) of a slide (4-1/1). • There should be a circumferential gap of 1 to
2 mm between barcode sticker’s outer edges and the edge of the barcode area. This is necessary for safe identification of barcode.
Fig. 4-1
Slide with barcode sticker
• Check that the barcode sticker does not
protrude from the slide edges, nor must it be affixed to part of the cover slip surface.
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OPERATION Preparing Slides and Magazines
Carl Zeiss
4.1.2
MIRAX SCAN
Inserting Slides into a Magazine Only original Carl Zeiss magazines are allowed for used with the MIRAX SCAN! Two magazine versions are available: a) standard magazines (415000-0100-000) and b) universal magazines with a metal bottom (415000-0102-000). The two versions differ in the types of slides they can handle (refer to 4.1).
The magazines are designed to hold a maximum of 50 slides. • Push slide (4-2/1) into the magazine (4-2/3) with
its barcode end (4-2/2) first. • Several slides should be inserted into a
magazine in a gap-less order, beginning from the left end. A magazine which is not completely filled is likely to topple over when being inserted or loaded. This can be prevented by filling with empty slides.
For transportation of a filled magazine without its cover in place (4-2/4), for example, for introducing it into, or removing it from, the MIRAX SCAN, the magazine should be slightly tilted to its closed side, to prevent the slides from falling out.
Fig. 4-2
Inserting slides
Whether slides will be safely seated and be able to perform guided motion in a magazine depends on the cleanness of that magazine. For this reason, one should make sure that all selected magazines are free from dust (compressed air may be used for cleaning) and free from glass breakage and other mounting media residues.
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MIRAX SCAN
4.1.3
OPERATION Preparing Slides and Magazines
Carl Zeiss
Insertion and Removal of Magazines
The MIRAX SCAN has two pairs of guide rails (input stack (4-3/4) and output stack (4-3/3)) to facilitate the safe loading and unloading of magazines. Danger of crushing or pinching Do not place your hands or fingers into the input or output stack motion area, while a digitization process is going on.
Remove the cover (4-2/4) before you insert magazines!
Replace the cover (4-2/4) when a magazine is not required for operation or will be stored for a certain time. This is necessary to prevent soiling of and mechanical damage to the magazine or the slides.
• Install a completely filled magazine (4-3/1) into
the input stack (4-3/4) for digitization. The magazine’s gear rack (4-3/2) must make contact with the guide rails and its open side must face the scanner. Do not place a magazine into the output stack and refrain from removing slides already digitized within their magazine! • Let the magazine slide down on the guide rails,
until the magazine rests on the guide pins of the magazine stacker. Note that the input stack provides for a maximum capacity of six magazines which may be installed at the same time. • Once all its slides have been digitized, a
magazine is pushed up in the output stack (4-3/3) and can be removed by the operator.
Fig. 4-3
Inserting / removing a magazine
Remember that a maximum of six magazines may be contained in the input stack and the output stack at a time!
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SOFTWARE DESCRIPTION Starting and Terminating the Scanning Software
Carl Zeiss
Fig. 5-1
MIRAX SCAN
5
SOFTWARE DESCRIPTION
5.1
Starting and Terminating the Scanning Software
MIRAX software icon
• Double-click the program icon (5-1) on the
desktop. A MIRAX control software session starts. • Alternatively, trigger program with: Start f Programs f Carl Zeiss f Mirax Scan
As part of a start-up routine, all motors, the preview camera and the scan camera will be initialized. On successful initialization, the program will output a selection window (Fig. 5-2). The scanner is able to work in two modes for brightfield applications (Brightfield scanning): −
Automatic
−
Manual
If your MIRAX SCAN includes a fluorescence option, these modes will equally be available for fluorescence jobs (Fluorescence scanning) (refer to 5.3). Fig. 5-2
Selection window mode
It is recommended to use specimens with identical staining for a given magazine filling in Automatic mode.
Selections for digitization mode should be made following this general rule: Automatic should be used for digitizing a greater number of specimens. Manual should be selected: −
if only individual slides need to be digitized,
−
where contrast relations are critical due to specimen stainings and where ideal parameters need to be determined for subsequent use in Automatic mode.
• A running control program session can be terminated by clicking onto the cross in the mode selection
window.
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SOFTWARE DESCRIPTION Brightfield Applications
MIRAX SCAN
Carl Zeiss
5.2
Brightfield Applications
5.2.1
Digitizing Slides in Automatic Mode (Standard Procedure 1)
This work procedure should be applied when a greater number of slides with high-contrast stained specimens need to be digitized. A hematoxylin/eosin staining can be picked as an example. Turn MIRAX SCAN, PC and monitor on (refer to 3.5)
Launch MIRAX control software
Insert magazine with colored high-contrast slides
Select Brightfield scanning Automatic
Select Preview
Scanner settings in Preview Optimization with Brightfield scanning Manual mode applied to a greater number of slides with colored high-contrast specimens (refer to 5.2.2)
Enable Automatic thresholding
Select Barcodes
If affixed barcodes are compatible: Enable Read the barcode
No special designations available: Enable Automatically generated numbers
Special designations are available: Enable Manually specified barcodes, Enter slide ID into table
Select Normal work
Specify First slide and Last slide, Change Scan options if necessary
Select Start scan
Remove all magazines from output stack on completion of scan process
Terminate Brightfield scanning Automatic
Close MIRAX control software
Turn MIRAX SCAN, PC and monitor off (refer to 3.6)
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Graphical representation of software components: Italic + bold: Bold: Underline: Italic:
Main mode Submenu (Tab) Button Selection box
31
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
5.2.2
MIRAX SCAN
Preview Optimization in Manual Mode (Standard Procedure 2)
This procedure is appropriate when a greater number of slides with stained low-contrast specimens needs to be digitized. An immuno-histological staining is selected for example. Turn MIRAX SCAN, PC and monitor on (refer to 3.5)
LaunchMIRAX control software
Insert magazine with low-contrast stained slides
Select Brightfield scanning Manual
Select Normal work - Click Insert magazine - Select slide position (Current slide) - Click Insert slide (preview image is displayed) Select Preview
No
Select Manual thresholding Do you want to change existing threhold?
Click New - Assign name
Yes
Select and change threshold until area of interest/ specimen to be scanned is completely marked red
Click Remove slide
Click Remove magazine
Terminate Brightfield scanning Manual
Select Brightfield scanning Automatic
Select Preview
Select Manual thresholding - Select threshold
Graphical representation of software components: Continue with Barcodes selection in Brightfield scanning Automatic flow diagram (refer to 5.2.1)
32
Italic + bold: Bold: Underline: Italic:
Main mode Submenu (Tab) Button Selection box
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SOFTWARE DESCRIPTION Brightfield Applications
MIRAX SCAN
5.2.3
Carl Zeiss
Digitization of Slides in Manual Mode (Standard Procedure 3)
This work procedure is intended for individual slides. Turn MIRAX SCAN, PC and monitor on (refer to 3.5)
LaunchMIRAX control software
Insert magazine with slide(s)
Select Brightfield scanning Manual
Select Normal work - Click Insert magazine - Select slide position (Current slide) - Click Insert slide (preview image is displayed)
Select Preview
Select Manual threshold - Change threshold until specimen is completely marked - Delete areas you do not want to scan
Select Normal work
If a compatible barcode affixed: Click Read the barcode
If no barcode available: Enter slide name
Change scan options, if necessary
Click Start scan
Digitalisierungsvorgang beendet
Click Remove slide
Click Remove magazine
Remove all magazines from output stack on completion of scan process
Terminate Brightfield scanning Manual
Close MIRAX control software
Turn MIRAX SCAN, PC and monitor off (refer to 3.6)
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Graphical representation of software components: Italic + bold: Bold: Underline: Italic:
Main mode Submenu (Tab) Button Selection box
33
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
5.2.4
MIRAX SCAN
Brightfield scanning Automatic Mode
After a click onto Automatic, the display and dialog window for Automatic operation will open with these register cards (Fig. 5-3): −
Normal work:
Provides fundamental scanner settings and initiates scan process
−
Barcodes:
Setting and input options for identification of slides
−
Preview:
Settings for optimized preview images
−
Service:
Auxiliary functions to support operation control and maintenance 2
3
1
4
5
1 2 3 4 5
Dialog and function block for scanner functions and scanner settings Display field for camera images Preview image as recorded by preview camera (areas subject to digitization are shown in red color) Logsheet window with digitization process data Information field showing latest state of digitization process of currently processed slide and overall progress state
Fig. 5-3
Automatic dialog and display window
A click onto the cross in the title bar of the window will terminate Automatic mode operation. The mode selection window will turn active again. A slide which may be contained in the slide holder at this moment will automatically be pushed back into the magazine.
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MIRAX SCAN
5.2.4.1
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
Normal work Register Card
Normal work designates the register card with fundamental digitization functions. The following data can be entered and functions triggered here: • Specification of first slide in a magazine to be
digitized (First slide). • Specification of last slide in a magazine to be
digitized (Last slide). • On
selection of button Remove all, all magazines (input stack and loading area) will be transferred to the output stack. Fig. 5-4
Normal work register card
Fig. 5-5
Scan Settings
To save time, all magazines should be removed from the input stack before Remove all is clicked.
By clicking onto the Scan options button, you can open the Scan Settings dialog window (Fig. 5-5). It provides setting options for the digitization process. These setting values will be valid for all slides of a batch, which are to be digitized. Image compression and Scan settings allow parameter selections which will determine the resulting quality of a virtual slide. Fig. 5-5 shows preset values. A more detailed description of the various parameter setting options which are available in this window is contained in the following two tables:
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35
Carl Zeiss
SOFTWARE DESCRIPTION Brightfield Applications
MIRAX SCAN
The table below provides a more detailed explanation of Image compression and Scan settings: Parameter
Explanation
Image compression
Sets image format for individual image fields
JPG
Saves image fields as Joint Photographic Experts Group files (jpeg) with a certain degree of loss. The resulting quality can be adjusted with the quality slider button. Great values yield images of high image quality. Such files will, however, be quite big. Small values result in low-quality images and small files. The default setting of 90 % provides the best possible compromise of image quality and file size, with smaller value settings (e. g. 70%) still yielding image of a high quality level.
PNG
Saves the various images as Portable Network Graphics files (png). This method guarantees loss-free saving of image information. PNG was raised to the standard procedure in 2003 W3C (ISO standard ISO/IEC 15948:2003), also refer to BMP.
BMP
Provides loss-free saving of the various images as Windows bitmap files (bmp). Since the compression algorithm proves less effective with BMP than with PNG files, the resulting files are greater for the BMP option than for the PNG option.
Fine focus frequency
Allows one to define after how many in a series of snapshots fine focusing (focusing through a small Z-range in small steps) is to be performed. This setting will influence the speed of the digitization process, because a fine focus routine will be carried out on completion of a defined number of image fields and focusing is a time-consuming sequence. The default setting of 4 should be applicable to the majority of specimens. For a specimen with strong non-planarity, you should pick a smaller value for this parameter. The same applies to cytological specimens. A setting of “one“ will define that focusing is to be performed for each image field. Although this results in 100% focused image sequences, it also takes essentially more time to digitize.
Coarse focus frequency
Allows one to define after how many in a series of snapshots coarse focusing (focusing through a great Z-range accomplished in several steps) is to be performed. This setting will influence the speed of digitization, because a coarse focusing sequence will be carried out after a specified number of image fields and focusing itself is a time-consuming procedure. Coarse focusing takes more time than fine focusing. The default setting of 8 should be OK for most specimens. Basically, the statements for Fine focus frequency apply to this parameter. Typically, this setting should be twice as great as the setting for Fine focus frequency.
Scan map dilation (µm)
This setting can be used to extend the red masked area. This edge extension zone can be specified in µm. The default value is 250 µm.
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MIRAX SCAN
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
Minimal object level (%)
The MIRAX SCAN will only perform focusing for image fields which were found to include a structure. This setting defines a minimum required fill level of an image for a focus sequence to be triggered. The default setting is 10%. With low-contrast samples (e. g. hemalum/eosin staining of myocardial cells), there may be cases of a whole virtual slide not being properly focused, because of seeming failure to detect an object in any of the image fields. One should set this value to 0% in such cases.
Stitching
By turning the Stitched function on, the user defines that the various tiles of a digitized slide will seamlessly stitch together in a subsequent MIRAX Viewer session with no perceivable positive or negative overlapping. If this function is active, digitization will automatically work with a greater overlap, which leads to increased digitization time (about 27% longer than with this function in disabled state). The resulting files will also be bigger by as much. If this function is disabled, digitization time and file size will be optimal, but the resulting image may exhibit positive or negative overlap effects.
Save image in original Bayer size
If this option is on, the various image fields will be saved with native pixel resolution (0.23 µm per pixel with standard configuration). If it is disabled, you will work with reduced pixel resolution (0.32 µm per pixel for standard configuration), and the resulting files will be smaller (by about 40%).
Use saved compensation image
If this option is disabled, several reference images of empty slide areas will be recorded at the beginning of each digitization process for a slide for white balancing and shading. On the other hand, where slides almost fully covered by a specimen are used (smears/streaks), the automated search for empty slide areas is bound to fail in some cases. You should note that action to search for empty image fields is restricted to Cutting out the coverslip edge (refer to section 5.2.4.3). By turning this option on, you may use a previously recorded reference image (refer to section 5.2.5.4) as compensation image for mathematical setting off against the digitized fields.
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37
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
MIRAX SCAN
The following table provides explanations to the various selections which are available for the two parameters Create hierarchical path for slides and Scan AutoScope compatible slide: Parameter
Explanation
Create hierarchical path for slides
If this function is active, a slide’s assigned name or barcode will be saved under a specified path in a 2-component group stepped breakdown pattern. Example: Name of slide (Slide name): 080412 Path name (slide directory path): C:\Slides Complete path of digitized slide: C:\Slides\08\04\080412\ With this function disabled, no such stepped breakdown pattern is applied for saving, so the location to which the above sample is saved will be: C:\Slides\080412\
Scan AutoScope compatible slide
This control box must be selected for the output format to be compatible with different image analysis software packages (not AxioVision). If this option is on, graphical representation by the MIRAX Viewer will happen at reduced speed, i.e. this option should not be selected, unless necessary to allow for a specific subsequent image analysis procedure.
A target directory for a digitized slide can be defined via Slide directory path. A Browse button is available for conveniently choosing a directory via the special selection window. All parameter inputs will be saved and be available for reuse during the next software session. Once all desired parameter settings and file-related entries have been made, a digitization process can be triggered by clicking onto the Start scan button. Before initiating a digitization process, you should check for adequate memory space on the destination drive! Available capacity can simply be derived from the last line (Available disk space) of the information field of Current scan progress. A message reporting readiness to start a digitization process will appear (5-6). By acknowledging it with OK, one can trigger the digitization process. By pressing Cancel, one will prohibit the process. Fig. 5-6
38
Message after pressing Start scan
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MIRAX SCAN
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
Once the digitization process has started, the user will be asked if there are actually no magazines in the output stack (remaining magazines may have to be removed). If this dialog box was acknowledged, the lowermost magazine of the input stack will be transferred into working position and the first selected slide be pushed onto the slide holder and positioned by the slide loader so the preview camera is able to generate a preview image which is a necessary precondition for selection of the areas to undergo digitization. Besides, the preview camera creates an image of the barcode area that may serve as a working input for barcode interpretation. A running digitization process may be interrupted at any point by pressing the Stop scan button. Stop scan will be disabled unless a digitization process was triggered. If a running digitization process is interrupted by pressing the Stop scan button, the slide which is being digitized at this moment will be returned into its magazine. Following another click onto Start scan, the user has two resumption options, depending on the current slide position: − If the cancelled slide occupied position 1 in the magazine, a special message with available resumption options will appear.
• On selection of Yes, the magazine will be re-scanned beginning with position 1. • If No is clicked, the currently processed magazine will move into the output stack and the next
magazine will be loaded from the input stack. • Cancel will abort this dialog session.
− If the cancelled slide occupied any magazine position other than 1 (position 2 in the given example), another message with available resumption options will appear.
• Selection of Yes will resume digitization with the same slide (i.e. position 2 in this case). • If you select No, the currently processed magazine will be scanned beginning with position 1. • Cancel will abort this dialog session.
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39
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
5.2.4.2
MIRAX SCAN
Barcodes Register Card
The Barcodes register card is intended for setting of identification features to the various slides. Three possibilities are provided in the Numbering subarea: Read the barcode This option needs to be selected if there are affixed barcode labels and the recorded barcode area image is to be interpreted as barcode. Automatically generated numbers Automatically assigns an ID number to the current slide. Example: 2M10 (2nd magazine/10th slide)
The algorithm for automated number generation will assign identical names to slides in the same magazine slot and the same magazine each time a given magazine is refilled. For this reason, data regarding digitized slides must be separately saved before loading new slides into the MIRAX SCAN. Otherwise, the contents of directories with identical names will be overwritten with the data of newly digitized slides on acknowledgement of a relevant software prompt.
Fig. 5-7
Barcodes register card
Manually specified barcodes Slides with special names (e. g. names in handwriting) or barcodes which cannot be read by the system must be entered into the underlying table by manual instruction. A maximum of 50 slide names can be defined. On excession of that number, the software will change back to the Read the barcode mode. A name reflects the position of a slide in its magazine.
The Clear all barcodes button can be used to delete all previous names from a given list. Slide names may also be copied from the Windows clipboard to the first column under Barcodes. To achieve this, you need to click the Paste from clipboard button.
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MIRAX SCAN
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
Working with Optovars If the MIRAX SCAN is configured with Optovars (option), you may select a desired Optovar in the second column (Optovar) of the table, using the selection menu. This selection will be valid, regardless of the type of barcode option that was chosen under Numbering. As many as 50 Optovar-related entries can be selected. Where more than one magazine is used, currently valid Optovar entries will also be applied to the next magazines.
5.2.4.3
Preview Register Card
The Preview register card provides three options for defining a threshold value in its Preview selection field. A threshold setting defines the ranges for masking (shown red in software viewing screens). Only a masked area will then be digitized with high resolution: Automatic thresholding If this option is selected, an automatic software algorithm will be carried out for each preview image to define the ranges that will be digitized. This option may be applied to specimens with intensive staining. Manual thresholding This option allows one to choose between previously defined threshold values. Smaller threshold values result in a more sensitive scanning of the ranges due to be digitized (while, e. g. dirt or other impurities are preferentially recorded at the same time and digitized along with useful data). Although greater threshold values turn out to be insensitive to impurities, they may fail to mask desired object areas so these areas will not be included in subsequent digitization. This option is recommended for use with lowintensity stainings (e. g. immuno-histochemical stainings).
Fig. 5-8
Preview register card
Use saved preview With the help of this toolbar (Fig. 5-22) the user may select areas for digitization or deselect areas from digitization. Saved preview is the selection field for calling up a defined mask with Load.
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41
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
MIRAX SCAN
This option is suitable for a slide with small single objects which cannot be captured by the preview camera with proper resolution, for example, some cytological samples.
2
1
Depending on the threshold value setting, the edges of a coverslip will be identified as objects for digitization. Since the digitization of these edges is a time-consuming procedure which requires extra memory capacity of the hard drive, Cutting out the coverslip edge can be used if desired to eliminate these areas from digitization. If the function is enabled, a purple-color frame will be superimposed onto the slide (5-9/1). Since, normally, the position of a coverslip is reproducible, this function guarantees that only those of the masked areas will be digitized, which are located within a user-defined (rectangle) area, while other areas, even though they may have been masked, will not be digitized. In automatic mode, this rectangle cannot be changed. This is only possible in manual mode. Working in automatic, you are only able to turn this option on or off. All previously red masked objects outside of this frame will be faded out. This ensures that only those masked objects will undergo digitization that are located within this area.
1
2
Frame (all areas located outside of the frame line are not subject to digitization, for example, the edges of the coverslip) Edges of coverslip
Fig. 5-9
Cutting out the coverslip edge option
If option Filling holes on scanmap is active, all unmasked areas within a masked area will also be masked. As an example, this function may prove helpful where a specimen exhibits a contrast level that decreases from outside to inside. With default settings, it may occur that inner weak-contrast areas (e. g. flatly tissue) will not be identified as earmarked for digitization. This function also designates such areas as due for digitization.
If a specimen with options as described above was not identified as due for digitization (e. g. due to extremely weak contrast), you may encircle this specimen with a black marker pencil. If option Scanning area inside the marker is turned on, the area within the marker pencil line will be highlighted in red color and included in a subsequent digitization sequence.
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SOFTWARE DESCRIPTION Brightfield Applications
MIRAX SCAN
5.2.4.4
Carl Zeiss
Service Register Card
The Service register card allows you to enable certain control and maintenance functions. If a jammed slide causes the digitization process to be interrupted, you may click the Emergency remove position button in order to transfer that slide into a position where it can be accessed for error removal. Action described in the fault finding and elimination procedure (refer to table on page 70 et seq.) should not be initiated before the slide has reached this position. By pressing the Slide removed manually button, you can notify the software that a slide was removed manually. If the Show image check box is turned on, an image field which is currently being digitized will appear in the display field 5-3/2. Fig. 5-10
Service register card
Show image should only be turned on in exceptional cases when you work in Automatic mode, because the digitization process will become much slower as a consequence. To link the data of a digitized slide with a patient’s data base, one need to enable the entry options below Database.
5.2.5
Brightfield scanning Manual Mode
Manual mode is intended for digitization of single slides. It can also be selected for slides which are distinguished by e. g. low-contrast staining so the area for digitization must be determined manually. Use available register card functions to determine and define parameter settings as appropriate to achieve optimal digitization results. Once selected, these settings can be applied in Automatic mode. Following a click onto Manual in the mode selection window below Brightfield, the display and dialog window of the Manual mode will open with pertaining register cards (Fig. 5-11). These are: −
Normal work:
Fundamental scanner settings, loading and unloading of magazines and slides and triggering of digitization process
−
Preview:
Settings for optimized preview images
−
Focus:
Settings for object-related focusing sequences
−
Service:
Auxiliary operation and maintenance functions
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43
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
MIRAX SCAN
2
1
5
3 4 1 2 3 4 5
Dialog and function block with scanner functions and scanner settings Live image and camera image display field Sub-area informing about the progress of a running digitization Toolbar for editing of preview image and for manual positioning of slide in relation to optical axis Preview image recorded with preview camera (areas to be digitized are shown in red color)
Fig. 5-11
Manual dialog and display window
• Clicking onto the cross in the window’s title bar will terminate Manual mode. The mode selection
window turns active again. A slide which is contained in the MIRAX SCAN at that moment will be automatically returned into its magazine, as soon as a manual mode session is exited.
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SOFTWARE DESCRIPTION Brightfield Applications
MIRAX SCAN
5.2.5.1
Carl Zeiss
Normal work
Normal work is the register card that provides basic digitization functions. Data entry options or function trigger options are as follows: • With a click onto
, the lowermost magazine in the input stack will be transferred into the position for loading of the first slide.
• With a click onto
, a loaded magazine will move into the output stack.
• Current slide:
For entering the slot position of a slide to be loaded from a magazine. A desired position can be defined as a numerical input or proceeding step by step with the help of the arrow buttons. • By clicking onto
, the slide loader transfers a selected slide (Current slide) from its magazine to the specimen holder. A preview is automatically generated and shown as part of this sequence.
• A click onto
Fig. 5-12
Normal work register card
will return that slide into its magazine.
• Slide name:
This input field is available for manual entry of a desired slide name, under which data relating to this slide are to be saved. If a compatible barcode label is affixed on the slide, it will be automatically detected, once the Read barcode button was actuated. It will also appear in the Slide name display box. • Following a click onto the Scan options button, the Scan Settings dialog window will open. It
provides parameter options for digitization process settings (refer to page 35 et seq.). • To initiate digitization of a loaded slide, you need to click on the Start scan button.
If the selected slide is a typical representative of a greater lot of slides with approximately the same properties, it makes sense to switch to Automatic mode and continue operation with the parameters you have generated in Manual mode.
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SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
5.2.5.2
MIRAX SCAN
Preview Register Card
The Preview register card offers three options for threshold setting in its Preview sub-area. A given threshold setting defines which areas will be masked (shown red in the slide preview). Only these masked areas will be included in a subsequent digitization process at high resolution: Automatic thresholding If this option was selected, an automatic software algorithm will determine the areas eligible for digitization for each preview image. This option can be applied to specimens with intensive staining.
Fig. 5-13
Manual thresholding This option allows you to choose between previously set threshold values. Small threshold values result in a more sensitive scanning of the areas due to be digitized (but preferentially also recording dirt portions or other impurities and including them in subsequent digitization). Although greater threshold values are known to be insensitive to impurities, they may fail to mask and, hence, digitize some of the desired specimen areas.
Preview register card
If your threshold value settings fail to achieve satisfactory results, but you still do not want to change these thresholds, you may use Manual thresholding/New to generate a new threshold value. You can assign a user-defined name and value to this new threshold. Once generated, it will appear in the list.
Default Fig. 5-14
High
Low
Masking
Threshold values and masking
A desired threshold value can also be directly selected by calling up a given threshold name and changing the related threshold setting with the help of the arrow buttons in the Current threshold selection box. This option is recommended for stainings of little contrast (e. g. immuno-histo-chemical stainings).
Use saved preview Various toolbar resources are provided (Fig. 5-22) to the user for selection of areas to be included in or excluded from digitization. Working in the Saved preview selection box, one may save a newly defined mask via Save and call this mask up again via Load if required at some later point in time.
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MIRAX SCAN
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
This option appears suitable where slides have to be handled, which contain small single objects or areas of interests that cannot be resolved by the preview camera with adequate precision, for example, a given number of cytological samples. The edges of a coverslip will be detected by the preview camera and included as areas of interest to be digitized, depending on the particular threshold value setting (Fig. 5-14; preview image subtitled “Low”). Since the digitization of such edges is a time-consuming process that occupies extra memory capacity of the hard drive, you may use the Cutting out the coverslip edge function to eliminate these areas from digitization. If this function is active, a purple color frame will be superimposed onto the slide (5-15/1). Since, normally, the position of a coverslip cannot be reproduced, this function guarantees that only those masked areas will be included in digitization, which are located within a user definable area (rectangle), while excluding other areas from digitization, although these may have been masked. A rectangle can be enlarged or diminished by dragging with the mouse. To achieve this, position the mouse pointer on one of the rectangle’s lines, click with the mouse and change the rectangle’s size. All previously masked red areas of interest which are now located outside of the altered frame line are thus eliminated, and solely the masked areas within the new boundary frame will be digitized.
2
1
If option Filling holes on scanmap is active, any nonmasked area within a given masked area will also be masked. This function may prove helpful e. g. where a specimen exhibits a contrast that decreases from the outside to the inside. When you work with default settings, it may happen that an inner area of little contrast (e. g. flatly tissue) is interpreted as not selected for digitization. In such cases, the function will mark these areas as due for digitization.
If none of the options which have been described above manages to identify a given specimen as wanted for digitization (e. g. extremely weak contrast), there is still a possibility to encircle the specimen in question with a black marker pencil. With option Scanning area inside the marker active, the area within the marker pencil line will be masked red and selected for digitization.
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1
2
Frame (all areas outside of frame will be excluded from digitization; including, e. g. the coverslip edges) Edges of coverslip
Fig. 5-15
Cutting out the coverslip edge option
47
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
5.2.5.3
MIRAX SCAN
Focus Register Card
On selection of the Focus register card (Fig. 5-16), you may make online adjustments as required during a running digitization process in manual mode. You can also work with the focus tool in offline mode. The Live sub-area enables a live image of the scan camera, once the Live button is turned active. This live image is displayed in the live image and camera image display field (refer to section 5.2.6). This option has no effect on a running digitization process and no live image will be displayed. If this is required, you need to select option Show image in the Service register card. Focus is the sub-area for setting restrictions to the focus range. If Limiting the range is active, you may define a lower focus range limit via Lower limit and an upper focus range limit via Upper limit, using the respective arrow keys. This function may prove necessary if, as a result of a soiled coverslip surface, focusing is targeted on a faulty spot on the coverslip surface rather than the actual specimen you want to digitize. With the help of button Set current you can set the Lower limit value to the current focus value (1568 in the given example) –32 and the Upper limit value to the current focus value +32. Clicking of the Auto focus button will initiate a focusing sequence in the image marker position. For Auto focus, the live image display should be turned off, because this function will reduce the processing speed of any other function that runs concurrently. The Step size selection box allows you to define a manual focus step size with the help of the two arrow buttons. Fig. 5-16 Focus register card The blue vertical arrow buttons are intended for manual focusing. This will have no influence on the way slides are digitized in automated mode. With the mechanical (cross) stage function (Fig. 5-22/9) in active state, a slide can be viewed like under a microscope. As a necessary precondition for this, the Live button must also be active. Furthermore, the Focus register card may include a possibility to work with an Extended focusing function. This extended focus functionality is provided as an option.
48
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SOFTWARE DESCRIPTION Brightfield Applications
MIRAX SCAN
Carl Zeiss
If active, it will capture several images in different focus planes for each image field. The regions of strongest contrast which belong to a given image are combined into an image that will contain the maximum contrast portions of all images recorded for this image field. This method guarantees a maximum in depth of focus. While exerting no influence in terms of the file size, it does have an impact on digitization speed, because a set of images has to be shot and mathematically combined into a single image. Once the increased depth of focus function was turned on via the Extended focusing control box, you may determine a desired number of focus planes via the Z level count selection box. The currently valid focus value (defined by z-value as determined by auto-focusing) is always interpreted as the starting point and point of reference. A value of “5“ means that the resulting image will be calculated, using the current focus value, two over-focused images and two under-focused images as mathematical input. For this reason, you are advised to pick an uneven number for Z level count. The mutual spacing between the individual images in z-direction can be specified via Z step size. It designates the number of motor steps (one motor step roughly equals 0.2 µm). For settings as shown in the example of Fig. 5-16, the extended focus procedure is illustrated in Fig. 5-17.
5
Fig. 5-17
Graphical view of Extended focus process (with bright marking unfocused areas and dark marking focused areas)
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49
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
5.2.5.4
MIRAX SCAN
Service Register Card
The Service register card contains specific control and maintenance functions that can be turned active. If the Emergency remove position button was actuated, the MIRAX SCAN will move the slide holder into the position for handing over, i.e. the slide can be retrieved by an operator after the cover has been taken off (refer to section 6.2.5). On completion of this procedure, the system should be able to detect the absence of a slide by itself. If there are still problems in terms of the system suspecting a slide in the holder, you may click onto the Slide removed manually button, thus notifying the software that the slide has been removed. If the Show image control box is active, the currently scanned image field will appear in the live image or camera image display field (5-20/3). Fig. 5-18
Service register card
Unless there are exceptional circumstances, Show image should not be activated, because this will considerably slow down the digitization process.
Fig. 5-19
Acknowledge prompt for insertion of an empty slide
At the beginning of a standard digitization process, several reference images of empty slide areas are automatically scanned for white balancing and shading purposes. However, where such slides have to be handled, which are almost fully covered by a given specimen (e. g. smears/streaks), the automatic search routine for empty slide areas may fail in some cases, which can be concluded from the fact that the resulting virtual slides are inferior to their usual quality in terms of e. g. white balancing and shading (e. g. darker marginal section for each image display field).
Get new compensation image for main camera is the function for scanning a compensation (reference) image beforehand, which is later mathematically set off against the digitized image fields. The slide mounted for this purpose should closely resemble the slide/coverslip combination which is later used for actual digitization. On clicking of Get new compensation image for main camera, the user is asked if an empty slide is contained in the specimen holder (Fig. 5-19). If so, this must be confirmed with Yes by the user. This confirmation will initiate the procedure to generate a scan camera compensation image. The system will display a special window as soon as this procedure has finished.
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MIRAX SCAN
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
To make this function operational for digitization, you must activate the Use saved compensation image item in the scan settings via the Scan options button of the Normal work register card. If the preview image of a slide fails to deliver a satisfactory result, you should generate a new compensation image for the preview camera. This procedure is initiated by clicking onto the Get new compensation image for preview camera button. For this procedure to be successfully completed, the user should take care that no slide is contained in the MIRAX SCAN. If the system still finds the MIRAX SCAN to contain a slide, the slide will be transported back into its magazine. Database settings are not required, unless the virtual slides are to be linked with a database. This function is not enabled, unless or before there is a valid connection with a database.
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51
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
5.2.6
MIRAX SCAN
Display Field for Live Image or Camera Image
This display field can display live or camera images of the scan camera (Fig. 5-20).
1 1 2 3
2 Toolbar Status bar Live or camera image
Fig. 5-20
52
3
Display field for live image or camera image
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SOFTWARE DESCRIPTION Brightfield Applications
MIRAX SCAN
Carl Zeiss
The live image will only be displayed if there is no digitization process running at the moment. To enable display during digitization, the Show image option of the Service register card must be activated. Different actions for the displayed live image can be triggered with the toolbar, like zooming or determination of exposure time etc. (Fig. 5-21). However, these possibilities are not available for camera images during digitization. 1
2
3
4
1
5
6
7
8
2
3
Toolbar 1 2 3 4 5 6 7 8
Enlarges the live image Scales the live image down The live image is displayed in a way that one pixel on the monitor corresponds to one pixel on the camera chip. Changes the size of the live image in a way that it completely fills the display window area Displays or suppresses the display of the horizontal and vertical image bar with scaling. Activates red staining of all overexposed pixels Re-calculates the exposure time for the scan camera Activates a dialog window with which the current live image can be saved as a bitmap or JPEG image.
Status bar 1 2 3
Current position of the image mark related to the live image Red (R), green (G) and blue (B) value of current pixel Zoom factor of the current live image (1:1 corresponds to a zoom of 1.00)
Fig. 5-21
Toolbar and status bar display field for live image or camera image
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53
SOFTWARE DESCRIPTION Brightfield Applications
Carl Zeiss
5.2.7
MIRAX SCAN
Toolbar
Regardless of what register card is currently selected, the toolbar will always be displayed. The most important toolbar functions allow you to select the areas you want digitized or not digitized, when the area to be digitized area has to be selected manually (e. g. in the case of certain cytological specimens) or simply if unnecessary areas (e. g. dirt) are to be deleted. These functions are described in Fig. 5-22 under 3 to 8 and 11. These functions are helpful if the Preview register card was selected. The mechanical stage function (Fig. 5-22/9) activates the shifting of the slide relative to the optical axis. The shifting is controlled by clicking with the left mouse-key into the preview image. It is recommended to enlarge the preview image via scaling (Fig. 5-22/10) for a more simple navigation. The current position is displayed via a yellow cross. A click onto one of these symbols (Fig. 5-22/3, 4, 5, 6 or 7) disables this mode again.
1 1 2 3 4 5 6 7 8 9
10 11
3
4 5
6
7
8
9
10
11
Coordinates of cursor position (status display) Button for specifying the cursor position (mm or numbering) Button for selecting a filled rectangle Button for selecting a filled circle Button for selecting a free-hand line Button for selecting a filled polygon Button for selecting dots If changes were made in the preview image, a maximum of 40 changes can be deleted in step-by-step by clicking this button each time. Tool to place the image mark at any desired position on the slide by a click; when the tool is active the slide can be shifted continuously in two coordinates to the display system in the same way as for the mechanical stage of a microscope. The shift towards z-direction (focusing) must be done via the settings in the Focus tab. This function can be disabled again by clicking onto one of the symbols (3 to 7). Scaling for the preview image (selection in preset steps using the selection box) Processing mode for selected areas (in combination with the symbols 3 to 7): Not scanned: Selected areas will be deleted from the preview Scanned: Selected areas will be added
Fig. 5-22
54
2
Toolbar for area selection in preview window
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MIRAX SCAN
5.2.8
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
Preview
The preview area displays two preview images each depending on the selected register card: Preview register card
Fig. 5-23
Specimen preview image
This figure displays the specimen image, with a red mask to show the area being digitized and with a purple frame if Cutting out the coverslip edge is active.
5.3
Barcode area register card
Fig. 5-24
Barcode area preview image
This figure displays the barcode area image. With the help of checkbox Rotate it by 180 degree the image can be rotated by 180 degrees in cases when there is lettering upside down. This image will be saved together with the digitization data and will be available in the MIRAX Viewer.
Fluorescence Applications (Option)
The control surface for fluorescence application closely follows that of bright-field application. Therefore the following section is intended to provide a survey of the Fluorescence scan workflow and to deal with the features that are specific to fluorescence (refer to sections 5.3.1 and 5.3.2).
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Carl Zeiss
5.3.1
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
MIRAX SCAN
Scanning of Slides in Fluorescence scanning Manual Mode Turn MIRAX SCAN, PC, monitor and X-Cite illuminator on (refer to 3.5)
Encircle relevant scan areas with black marker pencil on slide
Trigger MIRAX control software
Insert magazine with slides
Select Fluorescence scanning Manual
Select Work - Click Insert magazine - Select slide position (current slide) - Click Insert slide (preview image is displayed)
Enter slide name
Close Scan Settings
Select scan filter. Filter 1 defines the master channel that will be used for focus map creation.
Select scanning mode: Fully automatic: Start scan triggers a scan process, with focus and exposure time automatically set. User controlled: The Parameter window opens: - If Use user defined focus is active, focus parameter settings can be modified. - If Use user defined exposure times is active, exposure times can be defined for different colorings /dyes
Note: Once parameters have been defined, you may use Start Scan to trigger a scan also in User controlled mode.
On completion of scan procedure: Click Remove slide
Click Remove magazine
Terminate Fluorecsence scanning Manual
Terminate MIRAX control software
Turn MIRAX SCAN off (refer to 3.6)
56
Graphical representation of software components: Italic + bold: Bold: Underline: Italic:
Main mode Submenu (Tab) Button Selection box
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MIRAX SCAN
5.3.2
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
Scanning of Slides in Fluorescence scanning Automatic Mode Turn MIRAX SCAN, PC, monitor and X-Cite illuminator on (refer to 3.5)
Trigger MIRAX control software
Insert magazine with slides
Define filter: Options > Filter settings
Select Fluorescence scanning Automatic
Select Barcodes
Are compatible barcodes affixed: Activate Read the barcode
No special names available: Activate Automatically generated numbers
Special names are available: Activate Manually specified barcodes; Enter slide ID in Table
Select Work
Make entry for First slide and Last slide; Change scan options as appropriate
Select Start scan
Retrieve all magazines from output stack on completion of scan process
Terminate Fluorescence scanning Automatic
Close MIRAX control software Turn MIRAX SCAN off (refer to 3.6)
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Graphical representation of software components Italic + bold: Bold: Underline: Italic:
Main mode Submenu (Tab) Button Selection box
57
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
5.3.3
MIRAX SCAN
Definition of Fluorescence Filters
If a new filter has been placed into the filter wheel, the user must make filter definitions at first. This is done before opening the actual working area of the fluorescence software by clicking on Options f Filter Settings (Fig. 5-2). The following selection window will appear:
Fig. 5-25
Filter Settings selection window
The individual functions are: Position of the filter in the filter wheel Designation of the filter (name) and its use as a filter (Use as filter control box) False color of image display in the MIRAX Viewer (can be initialized with a right mouse-click) Select channel (RGB) in which the respective image is to be displayed in the Viewer Calculates exposition times for defined channels / closes window
58
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MIRAX SCAN
5.3.4
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
Fluorescence Scanning Manual Mode
• After a click onto the Manual in the Fluorescence scanning selection area, the Manual fluorescence
scan display and dialog window will appear with the following input and dialog levels: Work
Basic scanner settings, loading and unloading of magazines and slides plus triggering of scan process
Hardwares
Live image, focus functions, determination of exposure time and filter selection
Service
For control and maintenance functions
Because specimens have poor contrast in Fluorescence scanning mode, this mode includes no automatic object finding process. Accordingly, the Preview register card has no assigned function.
• By clicking onto User defined the Setup register card can be displayed:
Setup
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Possibility of alternative/manual definition of focus and exposure time parameters
59
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
5.3.4.1
MIRAX SCAN
Work Register Card
The Work register card is the input and dialog level for basic scanner functions.
Fig. 5-26
Work register card
The following data can be entered and functions initialized: Scanning mode Provides the user with a choice between Full automatic and User controlled mode. In Full automatic mode, focus and exposure time are automatically determined by the program. The User controlled mode provides the user with the possibility to define focus and exposure times manually. Functions A click on the Insert Magazine button ( ) will move the lowermost magazine in the input stack into loading position. A click onto the Remove Magazine button ( ) will move the loaded magazine into the output stack. The position of the slide to be loaded is to be inserted in the Current Slide input field. Enter the position either in numerical form or step-by-step using the arrow keys. A click on the Insert Slide button ( ) will move the selected slide into a working position; a preview image is being generated. A click on the Remove Slide button ( ) will move the slide back into the magazine. The
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MIRAX SCAN
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
Read barcode button activates the barcode reading. Finally, you can start the scanning process with a click onto the Start Scan button. A click onto Stop scan will terminate the scanning process. Scan options A designation for the slide can be entered manually in the Slide name input field. If there is a compatible barcode, it will also be read automatically and the data displayed under Slide name, too. A click on the Scan options button will open the Scan Settings dialog window (Fig. 5-27).
Fig. 5-27
Scan Settings selection window
Under Scan settings you set parameters which determine image quality. Fig. 5-27 displays the preset parameters. By selecting Exposure time and Scanning algorithm, the user has the opportunity to choose between different fluorescence scanning processes. Via Slide Server Params you can enter data for saving a scanned slide.
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Carl Zeiss
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
MIRAX SCAN
The individual data items are explained in the following table: Parameter
Explanation
Jpeg quality
Saves image fields as Joint Photographic Experts Group files (jpeg) with a certain degree of loss. The resulting quality can be adjusted with the quality slider button. Great values yield images of high image quality. Such files will, however, be quite big. Small values result in low-quality images and small files. The default setting of 90 % provides the best possible compromise of image quality and file size, with smaller value settings (e. g. 70%) still yielding image of a high quality level.
Focus map creating step
Defines at what point in the course of focusing map creation focusing will start. This setting has an effect on the speed of the scanning process, because the scanning time increases with the number of focusing runs.
Maximum exposure time
Displays the exposure time that must not be exceeded.
Calculate exposure time for all spots individually
If selected this option, the program will calculate the exposure times for each field of view individually.
Use the same exposure time for all spots
The program uses one exposure time for all fields of view.
No filter changing on FOV
If you have selected this option, the whole specimen will be digitized with one filter at first. It is only then that filters will be changed for the multichannel digitizer.
Filter changing on FOV
In the case of multi-channel scans, filters can be changed here after each field of view (FOV).
Select filters This input field is available for selection of filters from the complete list of defined filters. Select the filter(s) for generating the focus map via the check boxes behind the filter pull-down menus. It should be a channel with an exposure time as short as possible, but also with an adequate covered area. For cell nuclei stained with DAPI i. e., select the blue channel.
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MIRAX SCAN
5.3.4.2
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
Hardwares Register Card
In addition to the functions for bright-field applications described in section 5.2.5.3 (Focus register card), there are two further function areas of importance for fluorescence applications: the Exposure input field or the Auto exp. button and the Filters selection field. Working in the Filters selection field, you must select an appropriate filter from the complete list of defined filters first. In the Exposure input field you can enter an appropriate exposure time or have the appropriate exposure time automatically determined with a click on the Auto exp. button.
Fig. 5-28
Input area of Hardwares register card
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SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
5.3.4.3
MIRAX SCAN
Setup Register Card
The Setup register card can be activated by clicking onto the User controlled button in the Work register card. This is the place where you can define focus and exposure time parameters manually.
Fig. 5-29
Input area of Setup register card
Once the Use user defined focus control box has been activated, the user has two selection options: Coarse focus This option is for setting a coarse focus value manually. A click on the Set value button will adopt the focus value displayed in the Hardwares register card. Interpolated focus If this option is selected, the coarse focus level will be calculated from three different focus points of the object. To do so, a manual focusing sequence of the object must be carried out at three points via the Hardwares register card. Once the correct focus value has been determined, it can be saved with a click onto the Store button. The software will then calculate a coarse focus level for the digitization process from three values determined in the same way as mentioned before. Nevertheless the focus map will be generated automatically. The user can only define the start parameters to increase the focus speed. After activating the Exposure control box the user can define the exposure time for the selected filters manually. At first the respective filter has to be selected from the Hardwares register card. A desired exposure time can then be defined with the Set value button.
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MIRAX SCAN
5.3.4.4
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
Preview Register Card There is no automatic object finding routine included in the Fluorescence scanning mode due to the poor contrast of the slides. For this reason, the Preview register card has no assigned function.
5.3.4.5
Service Register Card
The Service register card is accessible to users. It does not differ from that for bright-field applications (refer to section 5.2.4.4, Service Register card).
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65
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
5.3.5
Fluorescence Scanning Automatic Mode
5.3.5.1
Work Register Card
MIRAX SCAN
The Work register card in the Fluorescence scanning Automatic mode is a modified version of the function and input level described under 5.3.4.1. As already described in 5.3.4.1 the user can access the Functions, Scan options and Select filters subareas. Against section 5.3.4.1 however, the user has a Scanning input area at disposal for work. This area is intended for definition of the number of the first and the last in a batch of successively processed slides. All slides between these positions will be automatically scanned.
Fig. 5-30
66
Work register card in Fluorescence scanning Automatic mode
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MIRAX SCAN
5.3.5.2
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
Barcodes Register Card
The Barcodes register card provides options for slide identification settings.
Fig. 5-31
Barcode register card
Three options are available in the Numbering sub-area: Read the barcode This option should be activated where barcodes are affixed that can automatically be read. Automatically generated numbers The program automatically assigns an ID number to a currently processed slide. Example: 2M10 (2nd magazine/10th slide). With every reload action, the algorithm for generating automatic numbers always assigns to slides the same designation according to their location in the magazine. For this reason, the data of previously scanned slides must be separately saved before the device can be reloaded.
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67
SOFTWARE DESCRIPTION Fluorescence Applications (Option)
Carl Zeiss
MIRAX SCAN
Manually specified barcodes Slides with special designations or barcodes must be entered into the table below manually. A maximum of 50 slides may be defined. The software will then switch back to Read the barcode mode. Any designations which may already exist in the list may be deleted with the help of the Clear all button.
5.3.5.3
Preview Register Card Fluorescence scanning mode includes no automatic object finding routine due to poor contrast of the specimens. The Preview register card has no assigned function for this reason.
5.3.5.4
Service Register Card
The Service register card can be accessed by users. It does not differ from that of bright-field applications (see section 5.2.4.4 Service register card).
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MIRAX SCAN
PREVENTIVE MAINTENANCE, TROUBLE SHOOTING AND SERVICE Preventive Maintenance (Base unit)
6
PREVENTIVE MAINTENANCE, TROUBLE SHOOTING AND SERVICE
6.1
Preventive Maintenance (Base unit)
Carl Zeiss
Preventive maintenance for the MIRAX SCAN is limited to the following work items: • Turn power off after each MIRAX SCAN operating session and put on protective cover (to prevent
settling of dust or penetration of moisture). • Do not install the MIRAX SCAN in a room where there is moisture. Max. allowed humidity: < 75%. • Cover up exposed tubes with dust protection caps. • Breathe onto water-soluble pockets of contamination (coffee, cola, etc.) and wipe them off with a lint-
free cotton patch or a piece of cloth slightly moistened with water, to which a soft detergent may be admixed. • Use a cotton swab or a lint-free piece of cotton cloth together with special L optics cleaning solution
to wipe off stubborn oil- or grease-like contamination. This cleaning mixture consists of 90 volume% of gasoline and 10 volume% of isopropanol (IPA). These components are also knows as: Gasoline: surgical spirit, petroleum ether Isopropanol: 2-Propanol, Dimethylcarbinol, 2-Hydroxypropane For operation in moist and warm climatic zones, you should make sure that the MIRAX SCAN is installed in bright, dry and properly ventilated rooms with < 75% air humidity. Precision mechanical and optical instruments are threatened by fungal contamination of their surfaces if operating in any of the following environments: −
Relative air humidity > 75% prevailing for more than three days with temperatures between +15 C and +35 C.
−
Dark rooms without air flow.
−
Sedimentation of dust and fingerprints on optical surfaces.
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Carl Zeiss
6.2
PREVENTIVE MAINTENANCE, TROUBLE SHOOTING AND SERVICE Trouble Shooting
MIRAX SCAN
Trouble Shooting
Problem
Cause
Action for error removal
The MIRAX SCAN does not work
Electric power supply broken
24 V power supply is not on. • Turn power supply on. Control computer is not on. • Turn control computer on. • Check cable connections.
Control program was interrupted
Slide jammed
• Click Emergency remove position button to move slide into initial position. • Terminate control program session. • Turn control computer and 24 V power supply off and detach power cord connector. • Take protective covers off (refer to page 72). • Remove slide manually (refer to page 76). • Replace protective covers. • Reconnect 24 V power supply and control computer to line power supply. • Turn 24 V power supply on. • Turn control computer on. • Launch control program.
Magazine jammed
• Terminate control program session. • Turn control computer and 24 V power supply off. Pull power cord connector. • Remove protective covers (refer to page 72). • Remove magazine manually (refer to page 77). • If a jammed magazine cannot be removed, you should contact service personnel. • Replace protective covers. • Restore line power to connect 24 V power supply and control computer. • Turn 24 V power supply on. • Turn control computer on. • Launch control program.
Name of currently • Close virtual slide in MIRAX Viewer. selected slide for digitization already exists and is open in MIRAX Viewer
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MIRAX SCAN
PREVENTIVE MAINTENANCE, TROUBLE SHOOTING AND SERVICE Trouble Shooting
Carl Zeiss
Halogen lamp defect
• Replace halogen lamp (refer to page 74).
Virtual slide improperly focused almost across its entire surface.
Unsuitable setting for “Minimum object level (%)“
• Set the value for “Minimum object level (%)“ to “0“.
Poor image quality
Imaging errors
• Contact service.
Virtual slides in MIRAX Viewer exhibit poor stitching:
Scan camera not properly adjusted (e. g. due to loose fixture)
• Contact service.
Slide is often positioned with fault
Mech. guide error in transporting system
• Contact service.
Error message during scan camera calibration Image screen dark
• Check if faulty positioning disappears selection of a different type of magazine.
after
Preview image is too Invalid bright (flare/glare effects) compensation or too dark image for preview camera
• Record new compensation image for preview camera (refer to 5.2.5.4)
Digitization process is extremely slow
• Turn Extended focusing option off if not required.
Extended focusing option is on
Blurred image in Manual Focus range is on mode False focus range setting All single images exhibit a shading effect
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• Turn Limiting the range (refer to Fig. 5-16) off. • Change focus range setting.
Algorithm failed to • Record reference image with empty slide (refer to find empty image 5.2.4.1, Use saved compensation image) fields
71
Carl Zeiss
PREVENTIVE MAINTENANCE, TROUBLE SHOOTING AND SERVICE Trouble Shooting
6.2.1
MIRAX SCAN
Removing Protective Covers
For replacement of the halogen lamp (or to perform other maintenance work) and to interrupt a running digitization procedure because of slide jamming or magazine jamming, the protective covers must be removed from the MIRAX SCAN. This is necessary to eliminate a fault situation. Remember to terminate the scan program and turn power to the control computer and the 24 V power supply off before you remove the covers. Five bolts (6-1/3) are located on the bottom face of the baseplate (6-1/4). They attach the covers to the baseplate. • Begin by removing cover 1 (6-1/1). • Use an open-end wrench (W/F 10) (6-1/5) to
turn the bolts (6-1/3) on the lateral sides of the MIRAX SCAN by 90° anticlockwise, proceeding pair-wise (6-1/B). Use both hands to take cover 1 carefully off to the top then. Use caution to prevent contact between the safety rails (2-2/5) and the scan camera as you take cover 1 off. • Turn bolt at the front of the baseplate also by
90° anticlockwise and use both hands to carefully raise and take cover 2 off (6-1/2). • On completion of necessary maintenance or
Fig. 6-1
Removal of covers
repair work, the covers (cover 2 at first, then cover 1) must be put back into place and locked in their positions. This is achieved by turning the bolts clockwise (6-1/A). Make sure that no cables are squeezed as you replace the covers.
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MIRAX SCAN
6.2.2
PREVENTIVE MAINTENANCE, TROUBLE SHOOTING AND SERVICE Trouble Shooting
Carl Zeiss
Replacement of Fuses Make absolutely sure that the power cord connector is detached before you proceed to action for replacement of the fuse.
The line power inlet with fuse section is located at the back of the 24 V power supply. The fuse section contains two fuses of type T 2.5 A / H / 250 V. • Unplug power cord connector.
• Pull fuse holder (6-2/3) out to the front. Use a small screwdriver if necessary for convenience. • Remove fuses (6-2/2) from fuse holder and replace them with new fuses. • Push fuse holder (6-2/3) into fuse section (6-2/1) until mechanical stop position. • Plug power cord connector. Fig. 6-2
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Replacement of fuse
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6.2.3
MIRAX SCAN
Replacement of Halogen Lamp
• Turn power supply off and pull power cord
connector. • Take cover 1 off (refer to 6.2.1). • Hold lamp mount (6-3/4) with your hand. • Loosen knurled thumb screw (6-3/2) at the back
of the heat sink body (6-3/1), until the lamp mount can easily be pulled out from the bottom. Caution! Hot surface! Allow the lamp surface to cool down sufficiently. Wait for a minimum time of approximately fifteen minutes. • Pull defective lamp (6-3/3) out from the top and
replace it with a new lamp (000000-0467-436). Use care to prevent physical contact of the new lamp bulb with bare fingers during replacement action! • Carefully push the lamp mount into the heat
sink until mechanical stop position. Make sure that the groove at the lamp mount is properly oriented. Lock the lamp mount with the knurled thumb screw, once the mount is correctly positioned. • Replace cover 1 (refer to 6.2.1). • Plug power cord connector and turn power
supply on.
Fig. 6-3
Replacement of halogen lamp
6.2.4
Replacement of Lamp Module (for Fluorescence Option)
This section recites some extracts from the X-Cite 120 operating manual. For full information, notably, instructions regarding safety, you are strongly advised to consult that manual. No alignment is required for the lamp module. Accordingly, the module is at once operational after a lamp replacement.
Caution! Hot surface! Allow the lamp surface to cool down sufficiently. Wait for a time of at least twenty minutes.
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• Pull power cord connector. • Unfix screw in lateral cover plate of the lamp enclosure and remove plate from lamp enclosure. • Detach Intelli lamp cables and power cable from socket terminal in lamp enclosure. • Detach two-pole power cable from its terminal in the lamp enclosure. • Detach Intelli Lamp Sensor at the back of the lamp module from its terminal in the lamp enclosure. • Open lamp holder arm, pull the lamp out of its holder moving it along both guide edges of the lamp’s
own ceramic holder. The lamp will disengage from the spring-loaded clamp as you do this. • Carefully retrieve the new lamp module (000000-1313-162) from its transporting container. Hold the
lamp module only by its ceramic part. Incorrect handling may considerably reduce the lamp module’s useful life. Hold it by the ceramic part in all cases! Prevent physical contact with the lamp’s glass surface or the inside surface of the reflector under any circumstances. Skin oil is damaging to these parts. • Position the lamp so the two guide edges of its ceramic mount can mate with slot in the lamp holder.
The middle of the lamp should now fit into the spring-loaded clamp. The "This side out" label should point to the outside as the lamp is inserted. • Push the two guide edges of the lamp’s own ceramic holder into the mating recesses of the lamp
holder. The middle of the lamp will snap into the spring-loaded clamp. Close the lamp holder arm again. • Connect the four-pole Intelli Lamp Sensor to its terminal at the back of the lamp enclosure.
The Intelli Lamp connector will not fit unless installed in the right position. If it does not plug in, you should turn it around by 180º. • Connect the two-pole power cable to its terminal in the lamp enclosure wall.
The two-pole power cable connector will only fit if installed in the right position. If it does not move in, you should turn it around by 180º. • Press the Intelli Lamp cable and the power cable into their terminal jacks in the lamp enclosure. • Screw the lateral cover plate to the enclosure.
In the lamp was installed in a non-conforming manner, a symbol with a lamp crossed out will light steadily on the display screen as power is turned on to the MIRAX SCAN.
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6.2.5
MIRAX SCAN
Removing a Slide
• If a slide got jammed or has suffered breakage
during a digitization process, digitization must be aborted. Having done this, you should try clicking the Emergency remove position button in order to move the slide into a position in which it can easily be removed (refer to 5.2.4.4 and 5.2.5.4 respectively). Danger of crushing/pinching! Remember to cancel the running digitization process, terminate the software session and turn power off before you remove a jammed slide. • Remove
protective covers as described in section 6.2.1.
Fig. 6-4
Removing the slide loader
• Detach connector (6-4/5) from motor block
(6-4/6). • Push locking lever (6-4/1) to the left, push locking lever (6-4/7) to the right and keep both levers in this
position. • Seize the slide loader (6-4/2) by its motor block (6-4/6) and pull it back by an approximate length of
10 mm far enough for the guiding pin to disengage from the groove in the motor block. Then lift the slide loader out of its mounting base.
Fig. 6-5
Removing a slide
• Press clamping lever (6-5/2) down. This will release the slide’s position lock. • Retrieve slide (6-5/1) from the holder. Release clamping lever.
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• Hold slide loader (6-4/2) by the motor block (6-4/6) and push it inwardly (to the MIRAX SCAN), until
the guiding pin mates with the motor block groove again. • Place the slide loader (6-4/2) back into its mounting base and press it down to the mechanical stop
position, in which the locking lever must engage (6-4/1). Use moderate force to press the loader part opposite the motor in clamp direction (6-4/2), until this part mechanically engages, too. • Plug connector (6-4/5) into motor block (6-4/6). • Mount protective covers again (refer to 6.2.1). • Perform a software restart.
Please note that any manipulation performed on a mechanical component (e. g. slide loader) by the user must be followed by a complete MIRAX SCAN initialization routine (software restart).
6.2.6
Removing a Magazine from the Transporting System
• To retrieve a jammed magazine from the
transporting system, you must remove both protective covers as described in chapter 6.2.1 at first. Danger of crushing/pinching! Remember to cancel the running digitization process, terminate the software session and turn power supply off before you remove a jammed magazine. Check that the magazine is not tilted, i.e. if its sits on both horizontal guide rails. • If the magazine is found to be in horizontal
position, tilt plate (6-4/4) with the drive assembly for horizontal magazine drive motion to the front far enough for the driving gear (6-4/3) to disengage from the driving worm gear.
Fig. 6-6
Removing a magazine
• Once the plate is in this position, the magazine
can easily be pushed on the guide rails (6-6/2;3) to the left or to the right for removal from the transporting system. • If the magazine is found to be tilted because of twisted tappets (6-6/1), you should at first restore the
tappets to their initial position. They are correctly positioned if vertically aligned exactly one above the other. • To do this, turn the knurled wheel (6-6/4) by hand, until the tappets are in their initial position again
and the magazine flatly rests on both horizontal guide rails. You can now tilt the plate (6-4/4) and push the magazine on the guide rails (6-6/2;3) to the left or the right in order to remove it from the transporting system. Please note that any manipulation performed on a mechanical component (e. g. transporting system) by the user must be followed by a complete MIRAX SCAN initialization routine (software restart).
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6.2.7
MIRAX SCAN
Installing and Removing the Filter Module (for Fluorescence Option)
• Terminate the running control program session,
shut computer down, turn power off and pull power cord connector. • Turn power supply off and pull power cord
connector. • Turn X-Cite illuminator off and pull power cord
connector.
Fig. 6-7
Danger of crushing/pinching! Remember to cancel the running digitization process, terminate the software session and turn power off before you proceed with filter module installation or removal.
Installing and removing the filter module
• Remove
protective covers as described in section 6.2.1.
• Turn filter wheel, until the desired position
(6-7/3) can be accessed. The filter wheel has a stopper so it cannot endlessly rotate in the same direction. Turn the filter wheel always slowly and with care, reversing the direction of rotation when perceiving mechanical resistance. • For installation, hold the filter module by its handling pads (one on the right, one on the left lateral
side of the module), raise it at the front end and introduce the module (6-7/2) in forward tilted position into the rear spring-loaded clamps (6-7/4) at the filter wheel. Having done this, press the filter module down, until it safely engages with the front spring-loaded clamps (6-7/1) of the filter wheel. • For removal, slightly tilt the filter module out of its front spring-loaded fixtures at first, then pull it out
of the rear spring-loaded components and take it off. • Place the protective covers back again. • Plug the power connectors again. Turn on power to the power supply, the X-Cite illuminator and the
control computer. • Trigger the control program.
A newly added filter module requires a special entry to be made in the control software (see 5.3.3).
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6.3
PREVENTIVE MAINTENANCE, TROUBLE SHOOTING AND SERVICE Requesting Service
Carl Zeiss
Requesting Service
Unless expressly described in this manual as a user work item, work of any kind requiring intervention in mechanical, optical or electronic parts of the MIRAX SCAN, including intervention into its internal and its electrical system, may not be performed by anyone other than Carl Zeiss Customer personnel or specifically authorized expert personnel. To ensure that your MIRAX SCAN will remain optimally set and continues in a faultless operating condition over a longer period of time, we recommend that you enter into a Service and Maintenance Agreement with Carl Zeiss. For supplementary purchase orders or to request service, please contact your local Carl Zeiss representative. For more detailed information, you may also contact us at:
[email protected] http://www.zeiss.de on the Internet.
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MIRAX SCAN
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