3D Histech Pannoramic MIDI 1.16 User manual

PM1.16-UG-Rev1
Pannoramic MIDI
1.16
User’s Guide
January 16, 2013
Rev. 1

Pannoramic MIDI 1.16 User’s Guide
Contents
Disclaimer....................................................................................................................... 4
Declaration Of Conformity............................................................................................... 6
Character Formats and ymbols....................................................................................... 7
Notes Regarding Operational afety................................................................................ 8
Notes on Warranty........................................................................................................ 10
Terms and Abbreviations............................................................................................... 11
1 Product Description.................................................................................................... 12
1.1 Product Overview....................................................................................................................12
1.1.1 Intended Use..................................................................................................................................................12
1.1.2 eatures and Benefits.....................................................................................................................................12
1.1.3 Warning and Information Labels....................................................................................................................13
1.1.4 Base Unit........................................................................................................................................................14
1.2 System Overview......................................................................................................................14
1.2.1 Pannoramic MIDI system................................................................................................................................15
1.2.2 Hardware Options..........................................................................................................................................16
1.2.3 Control Software............................................................................................................................................18
2 Installation................................................................................................................. 20
2.1 Control computer ports...........................................................................................................20
2.2 Connectors and cables.............................................................................................................21
3 Operating lides and Trays.......................................................................................... 23
3.1 Preparing Slides and Trays.......................................................................................................23
3.2 Affixing Barcode Stickers to Slides...........................................................................................24
3.3 Inserting and Removing Slides.................................................................................................26
4 oftware Description.................................................................................................. 28
4.1 Starting / Exiting Pannoramic MIDI Software Application.......................................................28
4.1.1 Starting the software......................................................................................................................................28
4.1.2 Exiting the software........................................................................................................................................29
4.2 Options.....................................................................................................................................29
4.2.1 Barcode Settings.............................................................................................................................................29
4.2.2 Image Compensation.....................................................................................................................................32
4.2.3 Microscope Settings.......................................................................................................................................35
4.2.4 External Application Call Settings...................................................................................................................39
4.3 Using Brightfield Manual Mode...............................................................................................40
4.3.1 Routine work tab............................................................................................................................................42
4.3.2 Scan Options window.....................................................................................................................................44
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Pannoramic MIDI 1.16 User’s Guide
4.3.3 Preview tab.....................................................................................................................................................46
4.3.4 Preview area scanned by preview camera.....................................................................................................49
4.3.5 ocus tab........................................................................................................................................................55
4.3.6 Service tab......................................................................................................................................................57
4.3.7 Display field and toolbar for live images........................................................................................................58
4.3.8 Start scan........................................................................................................................................................60
4.4 Using Brightfield Automatic Mode..........................................................................................60
4.4.1 Routine work tab............................................................................................................................................60
4.4.2 Barcodes tab...................................................................................................................................................62
4.4.3 Preview tab.....................................................................................................................................................66
4.4.4 ocus tab........................................................................................................................................................67
4.4.5 Service tab......................................................................................................................................................68
4.4.6 Start scan........................................................................................................................................................69
4.5 Using luorescent Manual Mode.............................................................................................70
4.5.1 Routine work tab............................................................................................................................................70
4.5.2 Scan Options...................................................................................................................................................75
4.5.3 Preview tab.....................................................................................................................................................79
4.5.4 Hardware tab..................................................................................................................................................82
4.5.5 Service tab......................................................................................................................................................86
4.6 Using luorescent Automatic Mode........................................................................................87
4.6.1 Routine work tab............................................................................................................................................87
4.6.2 Barcodes tab...................................................................................................................................................92
4.6.3 Preview tab.....................................................................................................................................................96
4.6.4 ocus tab........................................................................................................................................................97
4.6.5 Service tab......................................................................................................................................................97
4.7 Scan To Server..........................................................................................................................98
4.8 Using Profiles.........................................................................................................................105
5 Troubleshooting and Maintenance............................................................................107
5.1 Safety Information.................................................................................................................107
5.1.1 Cleaning the device......................................................................................................................................108
5.1.2 Cleaning the trays.........................................................................................................................................108
5.1.3 Preventive maintenance...............................................................................................................................108
5.2 Troubleshooting.....................................................................................................................109
5.2.1 luorescent Applications (optional).............................................................................................................111
5.3 Maintenance..........................................................................................................................112
5.3.1 Removing the protective covers...................................................................................................................112
5.3.2 Replacing the halogen lamp.........................................................................................................................114
5.3.3 Replacing Lamp Module (for luorescent Option).......................................................................................115
5.3.4 Removing a slide...........................................................................................................................................118
5.3.5 Installing and Removing the ilter Module ( luorescent Option)................................................................119
5.3.6 Transporting Pannoramic MIDI....................................................................................................................121
6 Technical Data........................................................................................................... 122
Index........................................................................................................................... 127
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Pannoramic MIDI 1.16 User’s Guide
Disclaimer
Copyright © 2001-2013 3DHISTECH Ltd.
All rights reserved.
Intellectual property related to the 3DHISTECH products are as follows:
EP 1,789,831; US 7,663,078; EP 2,024,772; JP 2009-512685; US 12/301,781; EP 1,644,767; JP 2007-
516451; US7,327,515; EP 1,994,398; JP 2008-557835; US 12/281,566; U0700210; US 6,246,785;
HU0900142; HU0700404; PCT/HU2007/000065; EP 08762668.5; US 12/663,537;
PCT/AT2006/000492; JP 2008-542552; EP 06817469; US 12/095,545; PCT/AT2006/000493; EP
06817470.5; US 12/095,596; HU0900741; US 61/264,732; US 11/826,752; P0401870;
PCT/IB2005/050344; US 11/662,976; HU0700409; US 12/042,050; US 77/636,144 and 007502032.
The above mentioned granted patents, granted utility model, registered trademarks, pending
international and national patent applications and the other corresponding IP are the sole properties
of the 3DHISTECH Ltd.
3DHI TECH Ltd. is not liable for damage of whatever nature (including, but not limited to, general
or specific damage, indirect damage, consequential damage or incidental damage, including the
results of the analysis of the digitized slides, for example, change of health status related to
erroneous diagnosis from the digitalized slide(s)) that stems from or is associated with use of
Product, digitalized slides, quality of staining, quality of stained slides, quality of used method of
staining. 3DHI TECH Ltd. assumes no responsibility for the functionality and fault-free condition of
your “application programs” (Workflows, VBA macros, Commander scripts).
CAUTION
This product has not been approved or cleared as a medical device by the U.S. ood and Drug
Administration.
Do not use this device in close proximity to sources of strong electromagnetic radiation (e.g.
unshielded intentional R sources), as these may interfere with the proper operation.
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Pannoramic MIDI 1.16 User’s Guide
Third-Party Disclaimer (LibTIFF – TIFF Library and Utilities)
3DHISTECH Ltd. is not liable for damage of whatever nature (including, but not limited to, general or
specific damage, indirect damage, consequential damage or incidental damage, including damage
resulting from lost profits, interruption of business, loss of business information, pecuniary loss or
similar damage) that stems from or is associated with the incorporated part of this Product that is
made by Silicon Graphics Inc.
THE OFTWARE I PROVIDED “A I ” AND WITHOUT WARRANTY OF ANY KIND, EXPRE ED,
IMPLIED OR OTHERWI E, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF
MERCHANTABILITY OR FITNE FOR A PARTICULAR PURPO E.
IN NO EVENT HALL AM LEFFLER OR ILICON GRAPHIC BE LIABLE FOR ANY PECIAL, INCIDENTAL,
INDIRECT OR CON EQUENTIAL DAMAGE OF ANY KIND, OR FOR ANY DAMAGE WHAT OEVER
RE ULTING FROM LO OF U E, DATA OR PROFIT , WHETHER OR NOT ADVI ED OF THE PO IBILITY
OF DAMAGE, AND ON ANY THEORY OF LIABILITY, ARI ING OUT OF OR IN CONNECTION WITH THE
U E OR PERFORMANCE OF THI OFTWARE.
Further Information
or the latest information on 3DHISTECH products and services, please visit our website at the
following URL: http ://www.3dhistech.com .
Company Address: 29-33 Konkoly-Thege Miklos street, Building 6
1121 Budapest – HUNGARY
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Pannoramic MIDI 1.16 User’s Guide
Declaration Of Conformity
3DHISTECH Ltd. declares that the product Pannoramic MIDI slide scanner is designed and produced
with consideration of specified requirements according to the ISO 13485:2003 and IEC 61326-2-
6:2005 standards, and conforms to the directives and other standards listed below:
IEC 61010-1:2001 (ed. 2), “Safety requirements for electrical equipment for measurement, control,
and laboratory use – Part 1: General requirements”
IEC 61010-2-101:2002 (ed. 1), “Safety requirements for electrical equipment for measurement,
control and laboratory use – Part 2-101: Particular requirements for in vitro diagnostic (IVD) medical
equipment”
EN 55011:1998, Group 1, Class A, “Limits and methods of measurement of radio disturbance
characteristics of industrial, scientific, and medical (ISM) radio-frequency equipment”
This product has been tested to the requirements of CAN/CSA-C22.2 No. 61010-1, second
edition, including Amendment 1, or a later version of the same standard incorporating the same level
of testing requirements.
Conformity with Directive 98/79/EC is marked by on the Pannoramic MIDI device.
Conformity with Directive IEC 61010-2-101:2002 (ed. 1) is marked by on the product
labeling.
urther information may be obtained from the manufacturer:
3DHISTECH Ltd.
29-33 Konkoly-Thege Miklos street, Building 6
1121 Budapest – HUNGARY
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Pannoramic MIDI 1.16 User’s Guide Character Formats and Symbols
Character Formats and ymbols
Example Words or characters that appear on the screen. These include field names, screen
and window titles, push-buttons and menu names, paths or options.
Keys on the keyboard. or example, function keys (such as F11) or the Ctrl+M key
combination.
Example Cross-references within this document or to other documents.
Warning! It might cause irreversible damage or harm to the user of the product or the
product itself if this instruction is not followed.
Caution! It might cause the product to not work properly if this instruction is not followed
and alerts to a potential danger situation.
Note: Calls attention to some important features.
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Pannoramic MIDI 1.16 User’s Guide Character Formats and Symbols
Notes Regarding Operational afety
The below section of this User’s Guide contains information and warnings of a kind that must be
followed by owner/operator personnel.
Warning and advisory symbols which are used on the base unit of the Pannoramic MIDI and in the
section 1.1.3 Warning and Information Labels have the following meanings:
CAUTION
Disconnect mains plug before any kind of intervention into the device!
CAUTION
Crush hazard!
The Pannoramic MIDI, including any of its original accessory components, should not be operated in
any other way than described in section 1.1.1 Intended Use.
Any of the following notes should be strictly observed:
Caution!
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 authorized service personnel. All claims for warranty and warranty
services will be null and void in any such case.
Warning!
Insert the power cord plugs only into a grounding outlet. The protective action
must not be rendered ineffective by extension cables without protective
conductor. The Pannoramic MIDI has a built-in protection which must not be
rendered ineffective by extension cables without protective (earth-ground)
conductor.
Warning! The operation of the instrument in explosion-risk environments is not allowed.
Warning!
If protective devices are found to be ineffective, the Pannoramic MIDI must be
shut down and precautions must be taken to prevent unintended usage. or
necessary repair work or work to restore proper operating condition, you
should contact the 3DHISTECH Customer Service.
Note:
Electric power to the Pannoramic MIDI is supplied via an external mains power
supply unit. 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.
Warning! Check that your local line voltage is compatible with Pannoramic MIDI
specifications before you turn power on.
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Pannoramic MIDI 1.16 User’s Guide Character Formats and Symbols
Disconnect plug! Remember to unplug the power cord before you open the Pannoramic MIDI
base unit or replace a fuse!
Warning! 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.
Warning! Only connect external devices that are safety extra low voltage rated to the
instrument to avoid the risk of electrical shock.
Warning!
The Pannoramic MIDI 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.
Caution!
Dirt or dust may adversely impact the operating capability of the Pannoramic
MIDI. or this reason, measures must be taken to eliminate such influences to a
maximum possible degree. During periods of non-use, the Pannoramic MIDI
must be protected with a dust cover. Check that power is turned off before you
put the cover on.
Caution! Avoid touching the lamp bulb. Disconnect power and allow the bulb to cool
down by waiting for about 15 minutes before replacing it.
Crush hazard!
There is crush hazard in the movement area of the slide insert during operation.
Please note that the digitizing process has to be interrupted and the insert
moved via software to the output position before removing the insert.
Warning!
Clogged or covered ventilation slots may result in a heat build-up with a
damaging effect for the Pannoramic MIDI. Keep the ventilation slots always
unobstructed and do not insert or drop objects into a ventilation slot.
Warning! A defective Pannoramic MIDI is not classified as domestic waste. It must be
properly disposed in accordance with currently valid legal requirements.
Warning!
The Pannoramic MIDI may not be operated by other than properly instructed
persons. Operating personnel must be fully aware of the potential dangers
which a particular field of application involves. The Pannoramic MIDI is a
precision instrument which may suffer a significant reduction in operational
functions or even physical destruction following intervention performed in any
nonconforming manner.
Warning! If an X-Cite 120 illuminator is used, the corresponding warnings included in the
manufacturer’s operating manual have to be observed.
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Pannoramic MIDI 1.16 User’s Guide Character Formats and Symbols
Notes on Warranty
3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic MIDI to be free from faults
in material and workmanship at the moment of installation. Defects must be notified immediately on
identification and maximum efforts must be undertaken in order to minimize damage. 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) 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 actions which are explicitly described in this User’s Guide, you are prohibited from
performing any kind of maintenance or repair work at the Pannoramic MIDI. Only authorized
3DHISTECH Service personnel or specifically authorized representatives are allowed to handle repair
work. In case of malfunction contact 3DHISTECH Service Support first.
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Pannoramic MIDI 1.16 User’s Guide Character Formats and Symbols
Terms and Abbreviations
C V Comma Separated Value
FOV ield of View
NA Numerical Aperture
Virtual lide / lide A digital image of a thin glass plate on which specimens are mounted for
microscopic study:
a dynamic, interactive image that you can manage, save, magnify, zoom, name,
evaluate, annotate, mark, comment, send to a colleague electronically for co-
operation or advice, and so on.
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Pannoramic MIDI 1.16 User’s Guide 1 Product Description
1 Product Description
1.1 Product Overview
1.1.1 Intended Use
The Pannoramic MIDI is designed to use transmitted light and reflected light fluorescence to digitize
biological samples and specimens (typically histological sections). The target users of the product can
work for example, in education, research, industry or medical sectors.
Warning!
After each scanning make sure to inspect the digital slide for over-
exposed areas. In case the the slide is scanned based on improperly set
parameters, it can highly affect the diagnostic result because of
information loss.
1.1.2 Features and Benefits
The Pannoramic MIDI offers world class brightfield and fluorescent whole slide scanning on up to 9
channels. An outstanding 0.12 µm/pixel resolution is achieved with the 40×/0.95 NA (equivalent to
62× magnification) Carl Zeiss Plan-Apochromat objective.
Key features of the Pannoramic MIDI scanner:
•Up to 9 freely selectable color filters for fluorescence
•High-end fluorescent illumination device – Lumencor Spectra 7 Light Engine
•Multiband filter support
•Noiseless L scanning with the best L camera available – pco.edge
•New compensation method to create an entirely homogenous slide image
•12 slide automatic loading and scanning
•Improved permanent autofocus
•Small footprint
•Compact and robust device
•Good quality and stable manufacturing
•Barcode reading
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Pannoramic MIDI 1.16 User’s Guide 1 Product Description
Pannoramic MIDI is an optimal choice for customers who want to scan in brightfield and in
fluorescent mode where the quantity of scanned slides will be regularly over 10 slides per day. It has
the best price/performance ratio with a reliable loading/scanning mechanism.
1.1.3 Warning and Information Labels
The following figure contains the labels used on the Pannoramic MIDI main unit, the external mains
power supply unit, and the HXP 120 illuminator.
Figure 1 – Warning and information labels
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Pannoramic MIDI 1.16 User’s Guide 1 Product Description
1.1.4 Base Unit
The following figure shows the main parts of the base unit.
Figure 2 – Main parts of base unit
1. Protective covers
2. Slide tray
3. CIS VCC- 52U25CL scan camera
4. HXP 120 fiber-coupled illuminator (option)
5. HXP 120 illumination adapter (option)
6. iber optic cable
1.2 ystem Overview
The standard scope of delivery of the product includes the following hardware and software
components.
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Pannoramic MIDI 1.16 User’s Guide 1 Product Description
1.2.1 Pannoramic MIDI system
The following figure shows the main parts of the Pannoramic MIDI system.
Figure 3 – Pannoramic MIDI system overview
1. HXP 120 fiber-coupled illuminator (option)
2. 24 V power supply
3. Pannoramic MIDI base unit
4. Monitor
5. Mouse
6. Control computer
7. Keyboard
8. Slide tray
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Pannoramic MIDI 1.16 User’s Guide 1 Product Description
1.2.2 Hardware Options
Note:
The configuration of the control computer and monitor can vary
depending on the product order.
Cameras
AxioCam MRm Rev 3
1 CCD scientific, cooled, monochrome camera for
high quality, sensitive fluorescent applications.
CI VCC-F52U25CL
3 CCD camera for high-quality brightfield
applications allowing fast scanning.
pco.edge
Equipped with a high-quality sCMOS image sensor
for fluorescent applications allowing fast scanning
and an outstanding low read out noise. Cooled
with Peltier element.
tingray F146C IRF Medical camera
1 CCD camera for normal brightfield application
and entry level fluorescent applications.
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Pannoramic MIDI 1.16 User’s Guide 1 Product Description
Camera adapters
0.63× adapter 1× adapter
Warning!
The installation of the cameras in Pannoramic MIDI must be carried out
by trained professionals!
In any other case the warranty will be automatically voided. The
supplier or distributor is not liable for any damages caused by an
installation carried out by an unauthorized person.
Base Unit options
•Pannoramic MIDI Basic Scan Option / ast Option – base unit equipped with Stingray or CIS
cameras for Brightfield scanning (no fluorescent accessories included)
•Pannoramic MIDI Basic luorescence Option – base unit completely equipped with Stingray
or CIS VCC- 52U25CL camera for Brightfield scanning; with AxioCam camera and HXP 120
illuminator, trigger cable and filters for fluorescence scanning
•Pannoramic MIDI Advanced luorescence Option – base unit completely equipped with CIS
VCC- 52U25CL camera for Brightfield scanning, and with pco.edge camera and Lumencor
fluorescence illuminator, trigger cable and filters for fluorescence scanning
NOTE: In case Lumencor light source is ordered, the custom light source and filter modules
can be variable. or more information, please contact 3DHISTECH customer service.
Objectives
•Carl Zeiss Plan-Apochromat 20×/NA 0.8
•Carl Zeiss Plan-Apochromat 40× Corr/NA 0.95
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Pannoramic MIDI 1.16 User’s Guide 1 Product Description
Fluorescent Option for Pannoramic MIDI
luorescent unit (internal part)
HXP 120 luorescent illumination
unit (can be used with AxioCam
MRm Rev3 only)
Lumencor Spectra 7 Light Engine
illumination unit (can be used with
pco.edge camera only)
1.2.3 Control oftware
•Pannoramic canner control software
Optional:
•luorescence
•Extended focus
•Z-stack
•Barcode reader (licensed feature)
•Scan To Server
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Pannoramic MIDI 1.16 User’s Guide 1 Product Description
•Pannoramic Viewer software (fully functional)
Optional:
•CaseCenter
•Pannoramic Viewer TMA module
•3D Reconstruction module
•HistoQuant, NuclearQuant, MembraneQuant, Cyto ISHQuant, and DensitoQuant modules
•ImmunoScreener module
•E-School Encoder
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Pannoramic MIDI 1.16 User’s Guide 2 Installation
2 Installation
Warning!
The installation of Pannoramic MIDI must be carried out by a trained
professional!
In any other case the warranty will be automatically voided.
The supplier or distributor is not liable for any damages caused by an
installation carried out by an unauthorized person.
Only qualified service assistants are allowed to install the hardware and software. The product is
ready for use after installation.
2.1 Control computer ports
The following figure shows the location of the connectors in order to enable easier transportation of
the product for a short distance, by disconnecting cables and detaching hardware components from
each other.
Figure – Ports on control computer
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