mirax desk - ZEISS Mirax Downloadservice

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Scanner with manual slide feed (v1.9)
Operating Manual
MIRAX DESK
Carl Zeiss
COPYRIGHT / TRADEMARKS
MIRAX DESK
Knowledge of this manual is required for the operation of the instrument. Would you therefore please
make yourself familiar with the contents of this manual and pay special attention to hints concerning safe
operation of the instrument.
The specifications are subject to change; the manual is not covered by an update service.
©
Unless expressly authorized, forwarding and duplication of this document, as well as utilization and
communication of its contents are not permitted. Violations will entail an obligation to pay
compensation.
All rights reserved in the event of granting of patents or registration of a utility model.
All names of companies and products mentioned in this manual may be trademarks or registered
trademarks. 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 is not liable for the performance or use of these products.
MIRAX DESK was developed, produced and licensed exclusively for Zeiss by 3DHISTECH Kft./Hungary.
Issued by:
Carl Zeiss MicroImaging GmbH
P.O.B. 4041, 37030 Göttingen, Germany
Phone:
+49 (0) 551 5060 660
Fax:
+49 (0) 551 5060 464
E-mail:
[email protected]
www.zeiss.de
Number of this Operating Manual: B 46-0142 e
Date of issue: Version 1; 01.06.2007
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MIRAX DESK
CONTENTS
Carl Zeiss
CONTENTS
Page
1
INTRODUCTION ..................................................................................................................5
1.1
Notes on instrument safety ...................................................................................................5
1.2
Notes on warranty ................................................................................................................8
2
DESCRIPTION OF DEVICE....................................................................................................9
2.1
MIRAX DESK, overall view .....................................................................................................9
2.2
MIRAX DESK, basic unit ......................................................................................................10
2.3
Name and intended use ......................................................................................................11
2.4
Instrument description and main features............................................................................11
2.5
Warning and information labels ..........................................................................................12
2.6
System overview of MIRAX DESK single user solution ..........................................................13
2.7
System overview of MIRAX DESK network solution..............................................................14
2.8
Objectives, cameras and adapters........................................................................................15
2.9
Accessories .........................................................................................................................16
2.10
Power supply and light source .............................................................................................16
2.11
Software options.................................................................................................................16
2.12
Technical data.....................................................................................................................17
3
START UP ..........................................................................................................................20
3.1
First start up........................................................................................................................20
3.2
3.2.1
3.2.2
3.2.3
3.2.4
3.2.5
3.2.6
3.2.7
Device connections and controls .........................................................................................20
Basic unit ............................................................................................................................20
24 V power supply ..............................................................................................................21
Monitor ..............................................................................................................................21
Control computer ...............................................................................................................22
Scan Camera.......................................................................................................................23
Wiring of device components..............................................................................................23
Door ...................................................................................................................................23
3.3
Switching the device on ......................................................................................................24
3.4
Switching the device off......................................................................................................24
4
OPERATION.......................................................................................................................25
4.1
4.1.1
4.1.2
Preparing and loading slides................................................................................................25
Affixing the barcode sticker to the slide...............................................................................25
Inserting and removing a slide.............................................................................................26
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3
Carl Zeiss
INHALTSÜBERSICHT
MIRAX DESK
5
SOFTWARE DESCRIPTION ................................................................................................ 27
5.1
Software version ................................................................................................................. 27
5.2
Starting/exiting MIRAX control software.............................................................................. 27
5.3
Use of profiles..................................................................................................................... 28
5.4
5.4.1
5.4.2
5.4.3
5.4.4
Digitization of a slide (standard procedure).......................................................................... 29
Brightfield Scan Mode Manual ............................................................................................ 30
Display field for live or camera images................................................................................. 42
Toolbar for preview image .................................................................................................. 44
Preview ............................................................................................................................... 45
6
CARE, MAINTENANCE, TROUBLESHOOTING AND SERVICE........................................... 46
6.1
Instrument care................................................................................................................... 46
6.2
6.2.1
6.2.2
6.2.3
6.2.4
6.2.5
6.2.6
Troubleshooting.................................................................................................................. 47
Removing and reattaching the device cover......................................................................... 49
Changing fuses on the power supply .................................................................................. 50
Changing the halogen lamp................................................................................................ 51
Removing the slide.............................................................................................................. 52
Determining the barcode type (option)................................................................................ 53
Determining the pixel size ................................................................................................... 54
6.3
Requesting service............................................................................................................... 59
4
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MIRAX DESK
INTRODUCTION
Notes on instrument safety
1
INTRODUCTION
1.1
Carl Zeiss
The MIRAX DESK has been designed, produced and tested in conformity with the standards EN 61010-1
(IEC 61010-1) and IEC 61010-2-101, safety requirements for electrical equipment for measurement, control
and laboratory use, and the relevant requirements laid down in Annex 1 of EC Directive 98/79/EC.
The conformity to the cited EC Directive 98/79/EC is documented by the
sign.
This operating manual includes information and warnings that must be observed by the user.
The following warning and information symbols are used in this manual:
NOTE
This symbol designates a note that should be closely followed.
CAUTION
This symbol indicates a possible hazard to the instrument or system.
CAUTION
This symbol indicates a possible hazard to the user of the instrument.
CAUTION
Hot surface!
CAUTION
Disconnect the instrument from line power before opening it!
CAUTION
Risk of jamming the fingers!
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5
Carl Zeiss
INTRODUCTION
MIRAX DESK
The MIRAX DESK, including original accessories, must not be used for applications other than those
described in this manual.
Pay special attention to the following information:
The manufacturer cannot assume any liability for other applications of the instrument, including
those of individual modules or single parts. This also applies to any service or repair work that is
not carried out by authorized service personnel. In case of non-compliance, all warranty claims
shall be forfeited.
The instrument must not be operated in explosive environments.
When working with hazardous substances, observe the directions for intended and correct use,
and the relevant statutory safety precautions.
The power plug must be inserted in an outlet with a grounding (earth) contact. The protective
capacity must not be rendered ineffective by using an extension cable without a ground wire.
If protective devices are found to be ineffective, the instrument must be switched off and
secured against inadvertent operation. Please contact a Zeiss service agency or the Carl Zeiss
Microscopy Service to have the instrument repaired.
The MIRAX DESK is powered by a power supply allowing line voltages to be used in the range
of 100 to 240 V ±10 %, 50/60 Hz without any need to change the voltage setting on the
instrument.
Before switching on the instrument, check whether it is suitable for the available line voltage.
Always disconnect the instrument from the power outlet before opening it and changing the
fuses.
Only use fuses appropriate for the rated current. The use of makeshift fuses and short-circuiting
of the fuse holders are not permitted.
The MIRAX DESK is not equipped with any special devices for protection from corrosive,
potentially infectious, toxic, radioactive, or other substances that may be hazardous to health.
Make sure to observe all legal regulations when handling such substances, particularly the
relevant national accident prevention regulations. Decontaminate infectious materials after use.
Dust and dirt may impair the instrument’s performance. The instrument must therefore be
protected as far as possible from such influences and covered with the dust cover when not in
use. Always verify that the instrument is switched off before you cover it.
Avoid touching the lamp bulb. Always pull the power plug before changing the bulbs and allow
the instrument to cool down for some 15 minutes.
6
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MIRAX DESK
INTRODUCTION
Carl Zeiss
Never open the front door unless prompted accordingly by software. When you open the door
at any other time, make sure not to reach with your hands into the instrument to avoid the risk
of crushing your fingers.
The front door is equipped with an interlock switch. If the door is opened while a digitization
process is running, this process will be stopped instantly.
Clogged or covered ventilation slats may lead to heat build-up that might damage the
instrument and, in extreme cases, cause a fire. Always keep the ventilation slats clear and
ensure that no objects enter the instrument through the ventilation slats.
Defective instruments must not be disposed of with household waste. Dispose of the
instrument in compliance with the relevant legal requirements.
The instrument may only be opened by trained persons or service staff.
The instrument may only be operated by trained personnel who must be aware of the possible
dangers involved with operation and the particular application concerned. The MIRAX DESK is a
high-precision instrument that can be impaired in its performance or destroyed when handled
improperly.
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7
INTRODUCTION
Notes on warranty
Carl Zeiss
1.2
MIRAX DESK
Notes on warranty
The manufacturer guarantees that the instrument is free of defects in material and workmanship when
delivered. Possible defects must be notified to us immediately and steps be taken to minimize damage. If
notified of such a defect, the manufacturer is obligated to rectify it at his discretion, either by repairing
the instrument or delivering an intact replacement. No guarantee is provided for defects caused by
natural wear (wearing parts in particular) and improper use.
The instrument manufacturer shall not be liable for damage caused by faulty operation, negligence or
any other tampering with the instrument, particularly the removal or replacement of instrument
components, or the use of accessories from other manufacturers. Any such action shall lead to a forfeit
of all warranty claims.
With the exception of the work specified in this manual, no maintenance or repair of the MIRAX DESK
may be undertaken. Repairs may only be carried out by Carl Zeiss service staff or persons expressly
authorized by Carl Zeiss. In case of any malfunction of the device, contact your responsible Carl Zeiss
service agency at first.
8
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MIRAX DESK
DESCRIPTION OF DEVICE
MIRAX DESK, overall view
2
2.1
1
2
3
4
5
6
Carl Zeiss
24 V power supply unit
30"TFT monitor
Mouse
Image Analysis XEON Workstation
Keyboard
MIRAX DESK basic unit
Fig. 2-1
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9
MIRAX DESK, basic unit
Carl Zeiss
2.2
1
2
3
4
Scanner cover
Protection rail
Scan camera (in this example: Sony DFW-X710)
Door
Fig. 2-2
10
MIRAX DESK
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MIRAX DESK
2.3
Name and intended use
Carl Zeiss
Name and intended use
Manufacturer’s designation: MIRAX DESK
The MIRAX DESK digitizes biological patterns and specimens, and samples of human and animal tissue on
smooth slides in transmitted light.
Typical fields of application of the instrument include e.g.:
−
−
−
−
−
Hospitals
Medical practices
Universities
Industry
Research institutes
2.4
Instrument description and main features
The main features of the MIRAX DESK are:
− Robust and stable basic unit
− Intuitive operation via keyboard and mouse
− Manual loading of one specimen slide each
− Illuminator HAL 12 V, 5 W for transmitted light
− High-resolution scanner optics
− Identification of the slide by digitization of barcode area
− Automatic specimen recognition and digitization of detected objects on the slide
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11
Carl Zeiss
Warning and information labels
2.5
Warning and information labels
Fig. 2-3
Location of warning and information labels
12
MIRAX DESK
B 46-0142 e 06/07
MIRAX DESK
2.6
System overview of MIRAX DESK single user solution
Carl Zeiss
System overview of MIRAX DESK single user solution
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13
Carl Zeiss
2.7
14
System overview of MIRAX DESK network solution
MIRAX DESK
System overview of MIRAX DESK network solution
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MIRAX DESK
2.8
Objectives, cameras and adapters
Carl Zeiss
Objectives, cameras and adapters
Illustration
Description, technical specifications
The standard MIRAX DESK is equipped with a Plan-Apochromat
20x / 0.8 objective.
Plan-Apochromat 40x / 0.95 Korr objective (optional)
Sony DFW-X710 Fire Wire (MIRAX Basic Scan Option)
AVT Marlin F-146C Fire Wire (MIRAX Fast Scan option)
Without illustration
B 46-0142 e 06/07
Preview camera with LED white light background illumination and
incident light illumination
15
Accessories
Carl Zeiss
MIRAX DESK
The standard MIRAX DESK is equipped with a C-mount adapter 1x.
C-mount adapter 0.63x (optional)
2.9
Accessories
Illustration
2.10
Catalog No.
Barcode stickers
415000-0101-000
Power supply and light source
Illustration
Catalog No.
24 V power supply
–
HAL 12 V, 5 W
000000-0467-436
Catalog No.
MIRAX scanning module, extended depth of
sharpness
415010-0113-000
MIRAX module Barcode detection 1D and 2D
415010-0110-000
2.11
Software options
Illustration
16
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MIRAX DESK
2.12
Technical data
Carl Zeiss
Technical data
Dimensions (width x depth x height)
MIRAX DESK, basic unit .................................................................... approx. 267 mm x 500 mm x 252 mm
Control computer ............................................................................. approx. 206 mm x 560 mm x 440 mm
19” monitor ..................................................................................... approx. 420 mm x 240 mm x 490 mm
24 V power supply.......................................................................... approx. 170 mm x 300 mm x 110 mm
Weight
MIRAX DESK, basic unit ........................................................................................................ approx. 11 kg
24 V power supply.................................................................................................................. approx. 2 kg
Ambient conditions
Transport (in packaging)
Permissible ambient temperature ...................................................................................... -40 °C to +70 °C
Storage
Permissible ambient temperature ..................................................................................... +10 °C to +40 °C
Permissible relative humidity (no condensation)............................................................ max. 75 % at 35 °C
Operation
Permissible ambient temperature ..................................................................................... +10 °C to +40 °C
Permissible relative humidity ........................................................................................ max. 75 % at 35 °C
Altitude at installation site ..................................................................................................... max. 2000 m
Atmospheric pressure .................................................................................................500 hPa to 1060 hPa
Pollution degree ......................................................................................................................................2
Operating data
Intended site..........................................................................................................................closed rooms
Electrical protection class .......................................................................................................................... I
Protection type .................................................................................................................................. IP 20
Electrical safety ......................................................... in compliance with EN 61010-1 (IEC 61010-1) under
consideration of CSA and UL directives
Overvoltage category............................................................................................................................... II
Radio interference suppression ......................................................... in accordance with EN 55011 Class B
Noise immunity.............................................................................................in accordance with EN 61326
Input voltage, basic unit......................................................................................................... 24 V DC ±1 V
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17
Carl Zeiss
Technical data
MIRAX DESK
24 V power supply
Intended site .........................................................................................................................closed rooms
Electrical protection class .......................................................................................................................... I
Protection type .................................................................................................................................. IP 20
Line voltage..................................................................................................................... 100 to 240 V AC
Line frequency ............................................................................................................................. 50 / 60 Hz
Power consumption..................................................................................................................max. 50 VA
Secondary voltage ......................................................................................................................... 24 V DC
Secondary current ........................................................................................................................max. 3 A
Fuses ........................................................................................................ 2 x T 2.5 A / H, 250 V, 5 x 20 mm
Light source
Halogen lamp (transmitted light).......................................................................................... HAL 12 V, 5 W
Average service life of halogen lamp (000000-0467-436) ................................................................4000 h
Software
MIRAX DESK operation control ...................................................... included in MIRAX DESK delivery scope
MIRAX Viewer software................................................................. included in MIRAX DESK delivery scope
MIRAX scanning module, extended depth of sharpness (optional)..................................415010-0113-000
MIRAX module Barcode detection 1D and 2D................................................................415010-0110-000
MIRAX Viewer software multi-license (optional) ............................................................415010-0117-000
MIRAX Viewer TMA module (optional)...........................................................................415010-0107-000
MIRAX software Teleconsulting server (optional)............................................................415010-0108-000
MIRAX DESK, standard configuration
Objective .......................................................................................................... Plan-Apochromat 20x / 0.8
Camera ...........................................................Allied Vision Technologies Marlin 146C or Sony DFW-X710
Camera adapter .........................................................................................................C-mount adapter 1x
Slide identification:
Identification of slides via preview camera (TIS DFK21F04): Storage of barcode area as image and
interpretation of barcode label as character string; the following 1D and 2D barcode types can be
interpreted:
18
•
Code39 (ASCII encoding)
•
Code93 (ASCII encoding)
•
Code128 (UCC/EAN128) (ASCII encoding)
•
EAN8 (Numeric encoding)
•
EAN13 (Numeric encoding)
•
UPC-A (Numeric encoding)
•
DataMatrix (Numeric encoding, Alpha encoding, AlphaNumericPunc encoding, AlphaNumeric encoding,
ASCII encoding, IS08 encoding)
•
Maxicode (Encoding mode 2, 3, 4, 5, 6)
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MIRAX DESK
Technical data
•
MicroPDF417 (Standard encoding type)
•
PDF417 (Standard encoding type)
•
QR (QR code Model 1, 2 encoding)
Carl Zeiss
MIRAX DESK devices equipped with a Logitech QC 4000 Pro preview camera are provided with an
additional barcode reader because this preview camera does not save images of the barcode area. The
option for saving the barcode area as an image is missing in these devices.
The barcode reader is able to read 1D barcodes only.
Slide specifications
Dimensions:............................................ (24.6 to 26.0) mm x (75.0 to 76.2) mm; 0.9 to 1.2 mm thickness
........................................................................................................ recommended: colored barcode area
Image digitization
Sony DFW-X710 Fire Wire
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
Allied Vision Technologies Marlin 146C Fire Wire
1/2" 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, system requirements (minimum)
CPU..................................................................................................................................2 x Intel 2.6 GHz
RAM................................................................................................................................................... 2 GB
Hard disk ........................................................................................................................................ 130 GB
Connections ...........................................................................................................................2 x Fire Wire
............................................................................................................................................... 1 x USB 2.0
.............................................................................................................................................. GB Ethernet
Input devices .................................................................................................................. keyboard, mouse
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19
START UP
First start up
Carl Zeiss
3
START UP
3.1
First start up
MIRAX DESK
The basic unit is delivered packed in a wooden box and a polyethylene box with cardboard packaging.
Additionally, the following components are supplied separately: slides, tools, power supply, scan camera,
1x C mount adapter, cables (2x Fire Wire, 1x USB), and spare lamps.
Control computer and monitor are delivered in separate cardboard packagings.
Installation and first start up of the MIRAX DESK are carried out by Carl Zeiss service personnel who will
hand over the instrument in a fully operational condition.
Dispose of the original packaging properly or save it for storing the device during extended periods of
non-use or returning it to the manufacturer.
3.2
Device connections and controls
3.2.1
Basic unit
The connection panel at the rear of the instrument
contains the socket for the power supply cable
(+24 V DC) (3-1/1) of the 24 V power supply unit
(24 V) with power indicator LED (3-1/2) and the
socket for the trigger cable (3-1/3) for the scan
camera (for Sony camera only).
In addition, the MIRAX DESK has a port for the
MIRAX DESK USB cable (3-1/4) and a Fire Wire port
for the preview camera (3-1/5) to establish
connection to the control computer.
Fig. 3-1
20
Connectors on basic unit
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MIRAX DESK
3.2.2
START UP
Carl Zeiss
24 V power supply
The power supply provides the basic unit with
24 V DC.
The power switch (3-2/1) is located at the front of
the power supply.
The back panel contains the line power input
connector
(3-2/3)
with
integrated
fuse
compartment and the non-detachable power
supply cable (3-2/2) for connection to the basic
unit.
Fig. 3-2
3.2.3
Controls and connectors on 24 V
power supply
Monitor
Please consult the supplied separate manual for information on the connectors and the location of the
controls of the monitor.
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21
START UP
Carl Zeiss
3.2.4
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Fig. 3-3
22
MIRAX DESK
Control computer
Fire Wire port
DVD drive (RW)
DVD drive
3.5" disk drive
ON/OFF switch
2x USB port
Power input connector
Keyboard connector
Mouse connector
4x USB ports – use one of these ports to establish the connection to the MIRAX DESK basic unit
Fire Wire port – to be used for the connection of the preview camera (consider labels, if any)
Network connector
DVI port - to be used for connection of monitor
DVI port
Fire Wire port – to be used for connection to scan camera (consider labels, if any)
Connectors and controls of control computer
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MIRAX DESK
3.2.5
START UP
Carl Zeiss
Scan Camera
As scan camera can be used:
a) Sony DFW-X710 Fire Wire.
The connectors for the trigger cable (3-4/1) and
the video output (3-4/2), Fire Wire (IEEE
1394/iLink), are located at the back of the camera.
or
b) AVT Marlin F-146C Fire Wire
The connector for the video output port (3-4/1)
Fire Wire (IEEE 1394/iLink) is located at the back of
the camera.
3.2.6
Fig. 3-4
Connectors on Sony camera
Fig. 3-5
Connector on AVT camera
Wiring of device components
Establish the cable connections of the system
using the supplied cables and the connectors
shown in Fig. 3-1, Fig. 3-2, Fig. 3-3 and Fig. 3-4 or
Fig. 3-5.
Verify that all cable connections are tightly fitted.
Never connect defective cables, but contact Zeiss
Service for a replacement.
3.2.7
Door
At the front of the device, a door is located used for loading a specimen slide (4-3/1). When this door has
been pushed aside to the left, a slide can be loaded or removed, if this process was initiated via software
before.
The front door is equipped with an interlock switch, which instantly stops a running digitization
process when this door is opened.
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23
START UP
Switching the device on
Carl Zeiss
3.3
MIRAX DESK
Switching the device on
To power all system components, switch on 24 V power supply, control computer and monitor
separately.
• First, switch on the 24 V power supply at the power switch (3-2/1).
• Switch on the control computer by pressing its ON/OFF switch (3-3/5).
The operating system is being started.
• Switch on the monitor.
The device is now ready for operation.
3.4
Switching the device off
• Exit MIRAX DESK software.
• Shut down the control computer following the standard Windows procedure.
• Switch the 24 V power supply off at the ON/OFF switch (3-2/1).
• Switch off the monitor.
24
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OPERATION
Preparing and loading slides
MIRAX DESK
4
OPERATION
4.1
Carl Zeiss
You may use all slides and coverslips, which meet the following specifications:
Slides
Coverslips
Length:
75.0 to 76.2 mm
Length:
max. 50 mm
Width:
24.6 to 26.0 mm
Width:
max. 24 mm (recommended: 22 mm)
Thickness: 0.9 to 1.2 mm
Thickness: 0.13 to 0.19 mm (recommended: 0.17 mm)
The slides should have a colored area for the use of barcodes.
Thus, all slides may be used manufactured in compliance with the International Standard
ISO 8037/1.
The edges of slide and coverslip should be parallel.
When mounting the coverslip, care should be taken that no part of the coverslip juts out
beyond the slide.
4.1.1
Affixing the barcode sticker to the
slide
The barcode field (4-1/3) is captured by the
preview camera and displayed in software. When
affixing the label, take care to leave a blank margin
of 1 to 2 mm around relative to the barcode area.
The interpretation of the barcode as text string
requires the use of a software option that must be
purchased separately.
• Take the barcode sticker from the roll and –
taking care that it is crease-free – affix it to the
colored area (4-1/3) as shown in Fig. 4-1.
• Affix the barcode sticker (4-1/4) to the specimen
side (holding the coverslip) (4-1/2) of the slide
(4-1/1).
Fig. 4-1
Slide with barcode sticker
• The outer edges of the sticker should be
approximately 1-2 mm away from the edge of
the barcode area to ensure that the barcode
can be read reliably.
• The barcode sticker must not overlap the
coverslip and not extend over the edges of the
slide.
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25
OPERATION
Carl Zeiss
4.1.2
MIRAX DESK
Inserting and removing a slide
The MIRAX DESK features a semi-manual feed for one slide.
Inserting a slide
• In MIRAX control software, click on the
button (for the use of the software, see p. 27ff).
The specimen holder moves to the load/unload position.
• A message is displayed prompting you to insert
a slide (Fig. 4-2).
• Open the door (4-3/1) by pushing it to the left.
• Throw the fixing lever (4-3/2) to the left.
• Put the slide (4-3/4) onto the specimen holder
Fig. 4-2
Software prompt to insert a slide
(4-3/3) so that coverslip and label are on top;
then, push it in.
Take care that the slide is not canted, and that it rests perfectly horizontally on the stage.
• After insertion of the slide, throw the fixing lever to the right until it touches the slide thus fixing it in
position.
• Close the door by pushing it to the right.
The door closure initiates the reading of the barcode field of the slide and the capture of the preview
image of the specimen area, which is displayed in the control software.
Removing a slide
• By
a click on the
button, the
unloading of the slide is initiated and the
specimen holder moved to the load/unload
position.
• A message window informs you that you can
change or insert the slide now (Fig. 4-2).
• Open the door (4-3/1) by pushing it to the left.
• Throw fixing lever (4-3/2) to the left.
• Remove the slide (4-3/4).
• You
may either insert another slide (as
described above) or throw the fixing lever to the
right as far as it will go and close the door.
Fig. 4-3
Inserting/removing a slide
The front door is equipped with an interlock switch, which instantly stops a running
digitization process when this door is opened.
26
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MIRAX DESK
SOFTWARE DESCRIPTION
Software version
5
5.1
Software version
Carl Zeiss
The software description is based on version 1.9 of the control software for the MIRAX DESK. As
software is continuously improved, the screenshots shown in this chapter may differ from the current
version delivered.
5.2
Starting/exiting MIRAX control software
• Double-click on the program icon (Fig. 5-1) on the desktop.
MIRAX control software is being started.
Fig. 5-1
Program icon of
MIRAX software
Fig. 5-2
Mode selection window
• Alternatively, start the software with:
Start f Programs f Carl Zeiss f Mirax Scan
During program start, all motors, the preview camera and the
scan camera are initialized.
After successful initialization, the program displays a selection
window (Fig. 5-2); as the scanner can be operated only semimanually, the Manual mode is started immediately.
If you had exited the manual mode and want to reactivate it,
click on the Manual button.
If you want to exit the control software, click on the cross
button ( ) in the title bar of the selection window.
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27
Use of profiles
Carl Zeiss
5.3
MIRAX DESK
Use of profiles
The MIRAX control software offers the option of using predefined profiles. If no profile has been loaded,
the settings will be used as defined in the individual input and dialog fields.
Profiles are storing the following information:
Scan Mode
Brightfield
Scan Options
Fine focus frequency
Coarse focus frequency
Compression procedure: JPEG, PNG, or BMP; in case of JPEG: image quality in %
Use of a fixed compensation image: YES/NO
Use of Stitching: YES/NO
Use of the hierarchical path: YES/NO
Use of database: YES/NO + settings
Optimized image view in MIRAX Viewer: YES/NO
Use of Bayer mask: YES/NO
Determination of the area to be scanned
Use of threshold value: YES/NO + threshold value
Use of a fixed scan area: YES/NO + path to the image of the scan area
Use of the distance to smaller areas: YES/NO + size of the areas
Filling of holes: YES/NO
Use of marker: YES/NO + threshold value of the marker
Use of limitation (Use Selection box): YES/NO + size
Other settings
Limitation of focus range: YES/NO + lower limit/upper limit
Use of extended depth of sharpness: YES/NO + step size and number of levels
28
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Digitization of a slide (standard procedure)
MIRAX DESK
5.4
Carl Zeiss
This flow chart applies to a single slide.
Switch on MIRAX DESK, PC
and monitor (see 3.3)
Start MIRAX control software
Choose Routine work
Click on
(see 5.2.1)
Insert the slide (see 4.1.2)
Preview image is displayed
Choose Preview (see 5.2.2)
Choose Manual thresholding
- Vary threshold value until object is completely masked
- Delete regions not to be digitized (e.g. dirt spots)
Choose Routine work (see 5.2.1)
Enter a slide name
Change Scan options, if necessary
Click on Start scan
Digitization process is
complete
Click on
(see 5.2.1)
Remove the slide (see 4.1.2)
Exit Manual scan
Exit MIRAX control software
Switch off MIRAX DESK, PC and
monitor (see 3.4.)
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Presentation of software elements
Italic + bold:
Bold:
Underlined:
Italic::
Scan mode
Tab, dialog box
Button
Selection field
29
Carl Zeiss
5.4.1
MIRAX DESK
Brightfield Scan Mode Manual
The Manual Scan Mode (Fig. 5-3) allows the digitization of a single slide. By using the functions
provided on the various tabs, you can determine parameters and execute actions:
Following a click onto Manual in the mode selection window below Brightfield Scan Mode, the display
and dialog window of the Manual mode will open with pertaining tabs (Fig. 5-3):
−
Routine work:
Fundamental scanner settings, loading and unloading of magazines and slides,
administration of profiles, and triggering of digitization process
−
Preview:
Settings for optimized preview images
−
Focus:
Settings for object-related focusing processes
−
Service:
Auxiliary functions for operation and maintenance
1
5
3
4
1
2
3
4
5
Dialog and function block with scanner functions and scanner settings
Preview image recorded with preview camera (areas to be digitized are shown in red/orange color)
Toolbar for editing of preview image and for manual positioning of slide in relation to optical axis
Sub-area informing about the progress of a running digitization
Live image and camera image display field
Fig. 5-3
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.
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MIRAX DESK
5.4.1.1
Carl Zeiss
Routine work tab
Routine work is the tab that provides basic digitization
functions.
Data entry options or function trigger options are as
follows:
Inserting and removing slides
•
With the
button, the specimen holder is
moved to the load/unload position. In this position,
you can remove the slide and put in a new one. For
a detailed description, see Section 4.1.2.
Take care that the slide is not canted, and
that it rests perfectly horizontally on the
stage.
• Slide name:
This input field is available for manual entry of a
desired slide name, under which the image data
relating to this slide are to be saved. If a compatible
barcode label is affixed on the slide, it will be
Fig. 5-4
Routine work tab
Fig. 5-5
Scan Profiles field
automatically detected, once the
button was actuated. It will also appear in the Slide
name display box.
• The Scan Profiles field (separate option) is used to
administrate the profiles:
A click onto Save will save the current settings
(Fig. 5-5). The system will ask for a new profile name.
All existing profiles can be selected via the selection
menu and enabled by clicking onto the Load button.
The current profile will be overlaid at the bottom on
. The current profile
the left
will be deleted by clicking onto the Delete button.
• Following a click onto the
button, the
Scan Options dialog window will open. It provides
parameter options for digitization process settings.
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31
Carl Zeiss
MIRAX DESK
Image Encoding and Scan Settings allow parameter
selections which will determine the resulting
quality of a virtual slide. Fig. 5-6 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:
Fig. 5-6
32
Scan Options
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MIRAX DESK
Carl Zeiss
The table below provides a more detailed explanation of Image Encoding and Scan Settings:
Parameter
Explanation
Image encoding
Sets image format for individual image fields
JPEG
Saves image fields as Joint Photographic Experts Group files (jpeg) with a
certain degree of loss. The resulting quality can be adjusted with the JPEG
quality factor 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 80 % provides the best possible
compromise of image quality and file size, with smaller value settings (e. g.
70%) still yielding images 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 by W3C in 2003 (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 you to define after how many in a series of snapshots fine focusing
(focusing through a small z-range with few 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 is 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 you 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 is 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.
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Carl Zeiss
MIRAX DESK
Parameter
Explanation
Stitching
By turning the Stitching 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 automatically 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 automatic 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 Use selection box (refer to section 5.4.1.2). By turning this
option on, you may use a previously recorded reference image (refer to
section 5.4.1.4) as compensation image for mathematical setting off against
the digitized fields.
Optimized slide
visualization (MIRAX
Viewer version 1.9
required)
If this option is active, smaller image fields will be saved. This will increase the
efficiency, if the resulting slides are used for teleconsulting. The Viewer
version 1.9 is absolutely necessary for viewing these virtual slides. To
guarantee a backward compatibility, this option must be disabled.
The following table provides explanations to the various selections which are available for the Scanned
slide destination field:
Parameter
Explanation
Database
This is to enter the required information if a database interfacing is used.
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MIRAX DESK
Carl Zeiss
Parameter
Explanation
Directory
If this function is enabled, the virtual slides will be digitized into a directory to
be specified. A Browse button is available for conveniently choosing a
directory via the special selection window. If a non-existing path is specified,
this path will be created by the software on acknowledgement. This
indication will not be saved in the profiles.
Use hierarchical folder structure: 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\
All parameter inputs will be saved and be available for reuse during the next software session.
To initiate digitization of a loaded slide, you need to click on the Start Scan button.
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35
Carl Zeiss
5.4.1.2
MIRAX DESK
Preview tab
The Preview tab offers two options for threshold
setting. A given threshold setting defines which
areas will be masked (shown red and orange in the
slide preview). Only these masked areas will be
included in a subsequent digitization process at
high resolution:
Manual thresholding
A desired threshold value is selected directly by
changing the threshold setting with the help of the
arrow buttons in the Current threshold selection
box.
Small threshold values result in a more sensitive
scanning of the areas due to be digitized (but also
dirt portions or other impurities will be
preferentially recorded and included 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.
Fig. 5-7
Preview tab
Use saved preview
Various toolbar resources are provided (Fig. 5-16)
to the user for selection of areas to be included in
or excluded from digitization.
Working in the Use saved preview selection box,
you may save a newly defined mask via Save and
call this mask up again via Load if required at some
later point in time.
default
Fig. 5-8
36
high
low
Masking
Threshold values and masking
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MIRAX DESK
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.
Various colors are used in the slide preview to show the
user the latest state:
2
Orange (Scanned specimen area): These areas will be
digitized later at high resolution. They are recognized by
the selected threshold value (see above).
Red (Scanned area): These areas will be digitized later at
high resolution. They are defined by the user and not
directly derived from the threshold value (e.g. the filling of
holes or user-specified areas).
1
Blue (Marker pen): The system shows that a marker pen
has been detected here (is only indicated if the option
Scan marker specified area has been enabled). The inside
areas appear in red color and, consequently, will be
digitized.
Yellow (Specimen area not scanned): These areas have
been detected by the preview camera, but they will not be
digitized, for example due to their position outside the
selected area (frame; selection box).
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. 5-8; 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 Use selection box function to eliminate these areas
from digitization. If this function is active, a black frame
will be superimposed onto the slide (5-9/1). Since,
normally, the position of a coverslip can be reproduced,
this function guarantees that only those masked areas will
be included in digitization, which are located within a userdefinable area (rectangle), while excluding other areas
from digitization, although these may have been masked.
1
2
Frame (all areas outside the frame will
be excluded from digitization; e.g. the
coverslip edges)
Edges of coverslip
Fig. 5-9
Use selection box option
A rectangle can be enlarged or diminished by dragging
with the mouse. To achieve this, position the mouse
pointer on one of the edge lines, click with the mouse and
change the rectangle’s size. All areas of interest previously
masked red or orange which are now located outside the
altered frame line are thus eliminated, and solely the
masked areas within the new boundary frame will be
digitized.
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37
Carl Zeiss
MIRAX DESK
If option Fill holes in scan area is active, any non-masked 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
outside to inside. When you work with default settings, it may happen that an inner area of little contrast
(e. g. fatty tissue) is interpreted as not selected for digitization. In such cases, the function will mask also
these areas as due for digitization (red).
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 pen. With option Scan marker specified area active, the area within the
marker pen line will be masked red and selected for digitization.
By activating the Scan map dilation function, the red or orange masked area can be extended. This edge
extension is specified in µm. The value cannot be changed continuously, because the edge is extended
discretely by one image field of the camera each time. The default value is 250 µm (in the standard
configuration); i.e. the area detected by the preview camera (shown in orange and depending on the
threshold value) is extended by one image field (shown in red color).
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MIRAX DESK
5.4.1.3
Carl Zeiss
Focus tab
On selection of the Focus tab (Fig. 5-10), you may make online adjustments as required 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 5.4.2). 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 images during scanning in the Service tab.
Focus is the sub-area for setting restrictions to the
focus range. If Limit focus 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
(1584 in the given example) –32 and the Upper
limit value to the current focus value +32.
Clicking of the
button will initiate a
focusing sequence in the image marker position.
For
, the live image
display should be turned off, because
this function will reduce the processing
speed of any other function that runs
concurrently.
Fig. 5-10
Focus tab
The Step size selection box allows you to define a
manual focus step size with the help of the two
arrow buttons.
The blue vertical arrow buttons are intended for manual focusing. This will have no influence on the way
slides are digitized in automatic mode.
With the mechanical (cross) stage function (5-16/9) 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 tab may include a possibility to work with an Extended focus mode function. This
extended focus functionality is provided as an option.
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39
Carl Zeiss
MIRAX DESK
If active, it will capture several images in different focus planes for each image field. The regions of
strongest contrast which belong to given images of a z-stack 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 sharpness. 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 sharpness function was turned on via the Extended focus mode control box
(Fig. 5-10), you may determine a desired number of focus planes via the Number of focus levels 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 Number of focus
levels.
The mutual spacing between the individual images in z-direction can be specified via Focus step size. It
designates the number of motor steps (one motor step roughly equals 0.2 µm).
Fig. 5-11
40
Illustration of the process for the Extended focus function
(bright areas are unfocused areas; the darker areas are in focus)
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MIRAX DESK
5.4.1.4
Carl Zeiss
Service tab
The Service tab contains specific control and
maintenance functions that can be turned active.
If the Emergency Manual Slide Removal Position
button was actuated, the MIRAX DESK will move
the slide holder to the load/unload position. 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 images during scanning control box is
active, the currently scanned image field will
appear in the live image or camera image display
field (5-14/3).
Fig. 5-12
Service tab
Unless there are exceptional circumstances, Show images during scanning should not be
activated, because this will slow down the digitization process.
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).
Fig. 5-13
Acknowledge prompt for insertion
of an empty slide
New Compensation Image for Scan 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 New Compensation Image for Scan Camera, the user is asked if an empty slide is
contained in the specimen holder (Fig. 5-13). 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.
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 Routine work tab.
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41
Carl Zeiss
MIRAX DESK
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
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 device. To be on the safe side, the system will
ask the user to remove the slide. If no slide was inserted, the door must simply be opened and closed
again.
5.4.2
Display field for live or camera images
The display field for live or camera images shows images of the scan camera (Fig. 5-14).
1
1
2
3
2
Toolbar
Status bar
Live or camera image
Fig. 5-14
42
3
Display field for live or camera images
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MIRAX DESK
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 images during scanning option of the Service tab 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. 5-15). However, these possibilities are not available for camera
images during digitization.
1
2 3
4
1
5
6
7
9
8
2
10
3
Toolbar
1
2
3
4
5
6
7
8
9
10
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.
With this mode activated, the live image will always be shown with a frequency of at least 10 images per
second. If an exposure time of more than 100 ms is set, the pixel values will be multiplied accordingly (if an
exposure time of 200 ms is set, the pixel values will be multiplied by 2 and the system will reset the exposure
time to 100 ms), i.e. the resulting images are characterized by a higher noise level.
If this mode is active, the images will be taken with the user-specified exposure time.
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 at the mouse pointer
Zoom factor of the current live image (1:1 means that one pixel on the camera corresponds to one pixel on
the monitor, i.e. a zoom of 1.00)
Fig. 5-15
Toolbar and status bar display field for live or camera images
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43
Carl Zeiss
5.4.3
MIRAX DESK
Toolbar for preview image
Regardless of what tab 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 has to be selected manually (e. g. in the case of certain cytological specimens) or if unnecessary
areas (e. g. dirt) are to be deleted. These functions are described in Fig. 5-16 under 3 to 8 and 11. These
functions are helpful if the Preview tab was selected.
The mechanical stage function (5-16/9) 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 (5-16/10) for a more simple navigation. The current position is
displayed via a yellow cross. A click onto one of these symbols (5-16/3, 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 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. 5-16
44
2
Toolbar for area selection in preview window
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MIRAX DESK
5.4.4
Carl Zeiss
Preview
The preview area displays two preview images each depending on the selected tab:
Preview tab
Label area tab
Fig. 5-17
Fig. 5-18
Preview image of specimen
Preview image of barcode area
This figure displays the specimen image, with a This figure displays the barcode area image. With
red/orange mask to show the area being digitized the help of checkbox Rotate image by 180 degree
and with a black frame if Use selection box is active. 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.
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45
CARE, MAINTENANCE, TROUBLESHOOTING AND SERVICE
Instrument care
Carl Zeiss
6
6.1
Instrument care
MIRAX DESK
Care of the MIRAX DESK is restricted to the following operations:
• Switch off the instrument each time after use and place the instrument cover over it to protect it from
dust and humidity.
• Do not set up the instrument in a humid room; maximum humidity < 75 %.
• Remove water-soluble dirt (coffee, cola, etc.) by blowing on it and wiping it off with a lint-free cotton
cloth or a cloth moistened with water, to which a mild detergent may be added.
• Wipe off stubborn oily or fatty dirt, e.g. fingerprints, with a cotton swab or lint-free cotton cloth and
the optics cleaning solution L.
This cleaning solution consists of 90 vol% gasoline and 10 vol% isopropanol (IPA). The individual
components are also known as:
Gasoline:
Medical alcohol, petroleum ether
Isopropanol:
2-propanol,
dimethylcarbinol,
2-hydroxypropane
When using MIRAX DESK in humid climatic zones, ensure that the device is kept in a light, dry and wellventilated room with a humidity of < 75 %.
The risk of fungus growth on opto-mechanical instruments invariably exists in the following conditions:
−
Relative humidity > 75 % and temperatures between +15 °C and +35 °C for more than three days.
−
Installation in dark rooms without air circulation.
−
Dust deposits and fingerprints on optical surfaces.
46
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MIRAX DESK
6.2
Troubleshooting
Carl Zeiss
Troubleshooting
Problem
Cause
Remedy
MIRAX DESK does not
work.
Power supply is
interrupted.
24 V power supply has not been switched on.
• Switch on the power supply.
Control computer has not been switched on.
• Switch on the control computer.
• Check the cable connections.
Control software has
stopped.
Slide is jammed
and cannot be
removed through
the door.
• Exit the control software.
• Switch off control computer and 24 V power supply;
disconnect the power cable.
• Remove the device cover (see page 49).
• Remove the stuck slide by hand (see page 52).
• Reattach the device cover.
• Re-connect the power cables of 24 V power supply
and control computer.
• Switch on the 24 V power supply.
• Switch on the control computer.
• Start the control software.
Error message during
calibration of scan camera
The name of the
slide currently to
be digitized exists
already and the
respective file has
been opened in
MIRAX Viewer.
• Close the virtual slide in MIRAX VIEWER.
Halogen lamp is
defective.
• Replace the halogen lamp (see page 51).
Imaging error
• Contact a Zeiss service representative.
Image is black
Poor image quality
B 46-0142 e 06/07
47
Carl Zeiss
Troubleshooting
Virtual slides show poor
False pixel size
stitching in MIRAX Viewer: setting
Scan camera not
properly adjusted
(e. g. due to loose
fixture)
MIRAX DESK
• Proceed as explained in section 0.
• Proceed as explained in section 0.
• Contact service.
Slide is often incorrectly
positioned.
Guiding fault in
transport system
• Contact service.
Preview image is too
bright (glared) or too dark
Invalid
compensation
image for preview
camera
• Capture a new compensation image for the preview
camera (see section 5.4.1.4)
Digitization process is
extraordinarily slow
Extended focusing
option is activated
• Deactivate the Extended focusing option if it is not
needed.
Image is out of focus.
Focus range limit
activated
• Deactivate the Limiting focus range option (see
Fig. 5-10).
Wrong focus range • Change the focus range.
setting
All individual images show Algorithm cannot
a shading effect.
find any blank
image fields.
48
• Capture a reference image with a blank slide (see
section 5.4.1.1, New Compensation Image for Scan
Camera and section 5.4.1.4)
B 46-0142 e 06/07
Troubleshooting
MIRAX DESK
6.2.1
Carl Zeiss
Removing and reattaching the device cover
The cover of the MIRAX DESK must be removed if you want to replace the halogen lamp or take out a
jammed slide that caused a stop of the digitization process.
The device may only be opened by instructed persons or service technicians.
Before removing the cover, exit the control software, switch off the control computer and
the 24 V power supply and disconnect the power cables.
Fig. 6-1
Removing/reattaching the device cover
• Using an Allen screwdriver (6-1/3), unscrew both Allen screws (6-1/2) from the holes (6-1/1) located at
the sides.
• Then, carefully push the cover (6-1/5) horizontally frontward with light pressure until it can be
removed completely from the basic unit (6-1/4).
• When you have finished maintenance or repair work, reattach the cover. To this end, push it
horizontally towards the basic unit (6-1/4) until the two protruding guide pins (6-1/6) fit into the
corresponding recesses of the basic unit.
• Note that the rear part of the cover must be pushed over the top part of the blue basic unit (6-1/7).
B 46-0142 e 06/07
49
Carl Zeiss
Troubleshooting
MIRAX DESK
• To lock the cover in place, insert the screws again and fasten them.
Take care that no cables are squeezed when you attach the cover.
6.2.2
Changing fuses on the power
supply
Make sure to disconnect the power
cable before changing any fuse.
The power input connector with fuse compartment
is located at the back of the 24 V power supply
unit. The latter contains two T 2.5 A/H / 250 V
fuses.
• Switch off the power supply and disconnect the
power cable.
• Pull out fuse holder (6-2/3) frontward. Use a
small screwdriver for this purpose, if necessary.
Fig. 6-2
Changing fuses
• Remove the fuses (6-2/2) from the fuse holder
and replace them by new fuses.
• Push the fuse holder (6-2/3) back into the fuse
compartment (6-2/1) as far as it will go.
• Reconnect the power cable and switch on the
power supply unit.
50
B 46-0142 e 06/07
MIRAX DESK
6.2.3
Troubleshooting
Carl Zeiss
Changing the halogen lamp
• Exit control software, shut down the computer, switch it off and disconnect the power cable.
• Switch off the power supply and disconnect the power cable.
• Remove the cover (see 6.2.1).
Fig. 6-3
Changing the halogen lamp
• Hold the lamp holder (6-3/1) with your hand.
• Loosen the knurled screw (6-3/2) at the underside of the lamp holder as much as is necessary to easily
pull out the lamp holder frontward. Do not remove the screw completely to prevent it from falling into
the device. Screwing it back into place may then be difficult to do.
Caution – Hot surface!
Wait for the lamp surface to cool down.
Keep a cool-down time of approximately 15 minutes.
• Remove the defective lamp (6-3/3) and replace it by a new one (000000-0467-436).
When changing the lamp, avoid touching the replacement bulb with the bare fingers!
• Taking care that the groove at the underside of the lamp holder is correctly aligned, carefully push the
lamp holder into the heat sink as far as it will go. Finally, lock it in place by means of the knurled
screw.
• Reattach the cover (see 6.2.1).
• Plug the power cable of the power supply into the power outlet and switch on the power supply.
• Connect the power cable of the control computer to the power outlet and switch on the computer.
B 46-0142 e 06/07
51
Carl Zeiss
Troubleshooting
6.2.4
MIRAX DESK
Removing the slide
If a slide has got stuck during the process of
digitization, stop the process and, if possible, move
the slide holder to a position where the slide can
be
easily
removed
by
clicking
the
Emergency remove position button (see 4.1.2).
Crushing hazard! Before removing a
slide that got stuck, stop the process
of digitization, exit the software and
switch off the device.
If this is not possible or the slide got broken, follow
this procedure:
• Exit the control software, shut down the control
Fig. 6-4
Removing the slide
computer, switch it off and disconnect the
power cable.
• Switch off the power supply and disconnect the
power cable.
• Remove the cover as described in Section 6.2.1.
• Throw fixing lever (6-4/3) frontward to the left.
• Remove the slide (6-4/1) from the holder (6-4/2). If the slide got broken, make sure to remove all
pieces completely from the device.
• Swing fixing lever (6-4/3) back to the right towards the holder.
• Reattach the cover (see 6.2.1).
• Connect the power cable of the power supply to the power outlet and switch on the power supply.
• Connect the power cable of the control computer to the power outlet and switch on the computer.
After every manipulation of mechanical components, you must always perform complete reinitialization
of the device.
52
B 46-0142 e 06/07
MIRAX DESK
6.2.5
Troubleshooting
Carl Zeiss
Determining the barcode type
(option)
A software option is available for the MIRAX DESK
to read barcodes. First of all, however, the barcode
type to be used must be defined. Select for this
purpose Options from the main menu and then
the Barcode Settings function.
A window will appear (Fig. 6-5) where the user has
to click onto the
button to insert a
slide with the barcode to be specified. Now, the
barcode type used has to be enabled under 1D
Barcode Types or 2D Barcode Types. Once this has
been done, the barcode can be read by clicking
button – the barcode area
onto the
will be shown in the window and the read barcode
indicated under Barcode. If the selected barcode
type does not correspond to the barcode affixed to
the slide (i.e. the barcode has not been
recognized), another barcode type has to be
selected.
Fig. 6-5
Settings for barcode recognition
If the barcode cannot be read although the correct type has been selected, the image can be optimized
via the settings under Preprocess Barcode Image, until the barcode can be read.
If the barcode cannot be read in spite of having proceeded as described, please contact the
service to have the problem explored (e.g. barcode area out of focus).
A green frame will be presented. It marks the area to be used for the interpretation of the barcode. The
size and position of the frame can be changed with the aid of the mouse. This limitation is recommended
if two barcodes are located in the barcode area and the barcode to be used for identifying the slide shall
be specified.
If you have limited the area, make sure that the barcode is located precisely within this area.
The settings under Special Barcode Settings should not be changed.
The settings will be saved by clicking onto the Done button and the window will be closed.
B 46-0142 e 06/07
53
Troubleshooting
Carl Zeiss
6.2.6
MIRAX DESK
Determining the pixel size
If the stitching quality is inadequate (e.g. double contours at the edge of the image fields), an
improvement can be reached by redetermining the pixel size and the angle of the scan camera. Please
contact your local Zeiss service if the image quality does not improve by using this function.
If this calibration function is not correctly used, it may happen that the outcome of the
digitization process is inadequate. That is why this function has to be used with great care.
The pixel size calibration function is called up via the main
window under Options, clicking on Optovar Settings
(Fig. 6-6). The window opened now allows you to carry
out this calibration step by step. For this purpose, a slide
containing a specimen is used. The specimen should have
the following properties:
2
Fig. 6-6
Calling up Optovar Settings
a) an area of approx. 1 cm of the specimen should be
without holes and similar artifacts
b) hemalum/eosin staining
First, the specimen holder has to be moved to the
load/unload position by clicking onto the
button, so that the user can insert the slide.
Fig. 6-7
54
Overview of pixel size calibration
B 46-0142 e 06/07
MIRAX DESK
Troubleshooting
Carl Zeiss
The following steps must be performed one after another. You may call up the corresponding
information online by clicking on .
Step 1:
The camera type is taken from the configuration file and cannot be changed. Apart from that, the
camera adapter magnification is entered. As the camera adapter has not been replaced, this value need
not be changed either.
Step 2:
In this step nothing should be changed, because MIRAX DESK uses only one channel (channel 10). In this
channel, the check box under BF must be enabled. The numbers under µm X and µm Y cannot be
changed here, they serve for information purposes only.
Step 3:
This field allows you to select the position to be used for the subsequent measurements. In MIRAX DESK
no other position can be selected.
B 46-0142 e 06/07
55
Carl Zeiss
Troubleshooting
MIRAX DESK
Step 4:
These fields show the data for the position selected in step 3. Nothing has to be changed here if there
was no objective change. The Optovar magnification indicated is without any significance in the MIRAX
DESK device.
Step 5:
The system needs a start value in order to be able to calculate automatically the pixel size (Micrometer /
pixel X and Micrometer / pixel Y). The existing values can be used if the optical configuration (objective or
TV adapter) has not been changed. If an optical component has been changed, the new start pixel value
can be calculated.
For this purpose, the calculator has to be called up by clicking on the Calculator button:
In this window, the adapter and objective magnifications, as well as value 1 for the Optovar have to be
entered. A click on Calculate will initiate the calculation of the pixel size, the result of which will appear in
the fields of step 5.
Step 6:
This step is to specify the overlap of the image fields of the scan camera in X and Y direction. The default
value for either direction is 30 µm. These values should be changed only if it is absolutely necessary.
56
B 46-0142 e 06/07
MIRAX DESK
Troubleshooting
Carl Zeiss
Step 7:
Now, an area of the specimen must be defined which shall be used for the measurement. This is done in
the same way as for the definition of a region to be scanned in the Manual mode (see section 5.4.1). For
this purpose, the functions of the Preview tab can be used (see section 5.4.1.2).
Primarily, however, the preview functions should be used:
The functions can be used as described in section 5.4.3). First, the area to be digitized can be removed.
After that, the area to be scanned can be marked using the rectangle function. Care has to be taken that
2
an area of about 1 cm is marked.
After having marked the respective area, start the measurement by
button. This measurement may take
clicking on the
some time. Once it has been completed, the pixel sizes in X and Y
direction are updated (see step 2). You should keep the original
values in mind. If the change exceeds 1 %, the measurement has to
be repeated, because it has to be taken into account that this is an
iterative process. Apart from that, the camera rotation value is
updated (see step 7). Values > 0.5 % or < -0.5 % will be presented
in red color. Such values cannot be stored. In this case the camera
must be readjusted. Contact the service for this purpose.
B 46-0142 e 06/07
57
Carl Zeiss
Troubleshooting
MIRAX DESK
Step 8:
Finally, the changed values have to be written into the EEPROM of the device; click for this purpose onto
the Save button.
The functions under Preview, Focus and Service correspond to those described in the sections 5.4.1.2,
5.4.1.3 and 5.4.1.4. They are not directly needed for the calibration process.
58
B 46-0142 e 06/07
MIRAX DESK
6.3
Troubleshooting
Carl Zeiss
Requesting service
Except for the work described in this manual, all repairs to mechanical, optical or electronic components
inside the device and its electrical components may only be performed by Carl Zeiss service staff or
specially authorized specialist staff.
To ensure optimum setting and trouble-free function of your MIRAX DESK over a longer period of time,
we recommend that you enter into a service/maintenance agreement with Carl Zeiss.
For subsequent orders, or when service is required, please contact your local Carl Zeiss representative.
For additional information, contact us at
[email protected]
http://www.zeiss.de
on the
Internet
B 46-0142 e 06/07
59

mirax desk - ZEISS Mirax Downloadservice

Transcription

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