3D Histech Pannoramic DESK 1.20 User manual

PD120-UG-Rev1
Pannoramic DESK
1.20
User’s Guide
October 9, 2015
Rev. 1

Pannoramic DESK 1.20 User’s Guide
Contents
Disclaimer....................................................................................................................... 4
Declaration Of Conformity...............................................................................................
Character Formats and Symbols.......................................................................................7
Notes Regarding Operational Safety................................................................................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 Features and enefits.....................................................................................................................................12
1.1.3 Warning and Information Labels....................................................................................................................13
1.1.4 ase Unit........................................................................................................................................................14
1.2 System Overview......................................................................................................................15
1.2.1 Pannoramic DESK system...............................................................................................................................15
1.2.2 Hardware Options..........................................................................................................................................16
1.2.3 Control Software............................................................................................................................................17
2 Installation................................................................................................................. 19
2.1 Control computer ports...........................................................................................................19
2.2 Connectors and cables.............................................................................................................20
3 Preparing Slides.......................................................................................................... 21
3.1 Affixing arcode Stickers to Slides...........................................................................................22
3.2 Inserting and Removing Slides.................................................................................................23
4 Software Description.................................................................................................. 2
4.1 Starting / Exiting Pannoramic DESK Software Application......................................................26
4.1.1 Starting the software......................................................................................................................................26
4.1.2 Exiting the software........................................................................................................................................26
4.2 Options.....................................................................................................................................26
4.2.1 arcode Settings.............................................................................................................................................27
4.2.2 Image Compensation.....................................................................................................................................30
4.2.3 Microscope Settings.......................................................................................................................................32
4.2.4 Event Call Settings..........................................................................................................................................35
4.3 Using rightfield Manual Mode...............................................................................................38
4.3.1 Routine work tab............................................................................................................................................39
4.3.2 Scan Options window.....................................................................................................................................40
4.3.3 Preview tab.....................................................................................................................................................42
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Pannoramic DESK 1.20 User’s Guide
4.3.4 Preview area scanned by preview camera.....................................................................................................45
4.3.5 Focus tab........................................................................................................................................................51
4.3.6 Service tab......................................................................................................................................................53
4.3.7 Display field and toolbar for live images........................................................................................................54
4.3.8 Start Scan........................................................................................................................................................56
4.4 Scan To Server..........................................................................................................................56
4.5 Using Profiles...........................................................................................................................61
5 Troubleshooting and Maintenance.............................................................................. 2
5.1 Safety Information...................................................................................................................62
5.1.1 Cleaning the device........................................................................................................................................62
5.1.2 Preventive maintenance.................................................................................................................................63
5.2 Troubleshooting.......................................................................................................................63
5.3 Maintenance............................................................................................................................66
5.3.1 Removing the protective cover......................................................................................................................66
5.3.2 Replacing the halogen lamp...........................................................................................................................67
5.3.3 Removing a slide.............................................................................................................................................69
5.3.4 Transporting Pannoramic DESK......................................................................................................................70
Technical Data............................................................................................................. 72
Index............................................................................................................................. 7
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Pannoramic DESK 1.20 User’s Guide
Disclaimer
Copyright © 2001-2015 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/I 2005/050344; 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.
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 the
results of the analysis of the digitized slides, for example, change of health status related to
erroneous diagnosis from the digitized slide(s)) that stems from or is associated with use of
Product, digitized slides, quality of staining, quality of stained slides, quality of used method of
staining. 3DHISTECH 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. Food and Drug
Administration.
Do not use this device in close proximity to sources of strong electromagnetic radiation (e.g.
unshielded intentional RF sources), as these may interfere with the proper operation.
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Pannoramic DESK 1.20 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 SOFTWARE IS PROVIDED “AS IS” AND WITHOUT WARRANTY OF ANY KIND, EXPRESSED,
IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF
MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR ANY SPECIAL, INCIDENTAL,
INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND, OR FOR ANY DAMAGES WHATSOEVER
RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER OR NOT ADVISED OF THE POSSIBILITY
OF DAMAGE, AND ON ANY THEORY OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE
USE OR PERFORMANCE OF THIS SOFTWARE.
Further Information
For 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, uilding 6
1121 udapest – HUNGARY
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Pannoramic DESK 1.20 User’s Guide
Declaration Of Conformity
3DHISTECH Ltd. declares that the product Pannoramic DESK 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 DESK device.
Conformity with Directive IEC 61010-2-101:2002 (ed. 1) is marked by on the product
labeling.
Further information may be obtained from the manufacturer:
3DHISTECH Ltd.
29-33 Konkoly-Thege Miklos street, uilding 6
1121 udapest – HUNGARY
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Pannoramic DESK 1.20 User’s Guide
Character Formats and Symbols
Example Words or characters that appear on the screen. These include field names, screen
and window titles, push-button and menu names, paths or options.
Keys on the keyboard. For 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 DESK 1.20 User’s Guide
Notes Regarding Operational Safety
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 DESK 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 DESK, 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 DESK 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 DESK must be
shut down and precautions must be taken to prevent unintended usage. For
necessary repair work or work to restore proper operating condition, you
should contact the 3DHISTECH Customer Service.
Note:
Electric power to the Pannoramic DESK 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 DESK
specifications before you turn power on.
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Pannoramic DESK 1.20 User’s Guide
Disconnect plug!
Remember to unplug the power cord before you open the Pannoramic DESK
device.
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 DESK 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
DESK. For this reason, measures must be taken to eliminate such influences to a
maximum possible degree. During periods of non-use, the Pannoramic DESK
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 plug and let the lamp cool
down for about 15 minutes before replacing the lamp.
Crush hazard!
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.
Warning!
The front door is equipped with an interlock switch. If the door is opened while a
digitization process is running, the process will be stopped instantly.
Warning!
A defective Pannoramic DESK is not classified as domestic waste. It must be
properly disposed in accordance with currently valid legal requirements.
Warning!
The Pannoramic DESK 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 DESK is a
precision instrument which may suffer a significant reduction in operational
functions or even physical destruction following intervention performed in any
nonconforming manner.
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Pannoramic DESK 1.20 User’s Guide
Notes on Warranty
3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic DESK 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 the amount of
damage as small as possible. On receiving notice of a fault, the Product Manufacturer will be under
obligation to remove the fault, at his own option, either by providing adequate repair services or by
delivering a faultless product for replacement. No warranty will be accepted in cases of natural wear
(notably, wear and tear parts) or improper product handling.
The Product Manufacturer will refuse any liability in the event of damage resulting from faulty
operation, negligence or unauthorized intervention into the product, notably, from the replacement
of product parts or the usage of accessory parts from other manufacturers. Any such case will void
the user’s claim for warranty.
Except for action which is explicitly described in this User’s Guide, you are prohibited from
performing any kind of maintenance or repair work at the Pannoramic DESK. Only 3DHISTECH Service
personnel or specifically authorized representatives are allowed to handle repair work. In case of
malfunction, contact the 3DHISTECH Service Support first.
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Pannoramic DESK 1.20 User’s Guide
Terms and Abbreviations
CSV Comma Separated Value
FOV Field of View
NA Numerical Aperture
Virtual Slide / Slide 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 and comment, send to a colleague electronically for co-
operation or advice, and so on.
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Pannoramic DESK 1.20 User’s Guide 1 Product Description
1 Product Description
1.1 Product Overview
1.1.1 Intended Use
Pannoramic DESK is designed to use transmitted light to digitize biological samples and specimens
(histological sections, typically). The target users of the product can work for example, in education,
research, industrial, or medical sectors.
Warning!
After each scanning make sure to inspect the digital slide for over-exposed
areas. If the slide has been scanned based on improperly set parameters, it can
highly affect the diagnostic result because of information loss.
Warning!
Any modification to a hardware or software component of the PC will highly
affect the functionality of the scanner program.
1.1.2 Features and Benefits
The Pannoramic DESK offers world class brightfield whole slide scanning. An outstanding 0.12
µm/pixel resolution is achieved with the 40×/0.95 NA (equivalent to 80× magnification) Carl Zeiss
Plan-Apochromat objective.
Key features of the Pannoramic DESK Scanner are:
•3MP camera for barcode reading and preview image
•Improved permanent auto-focus
•Compact and robust device
•Good quality and stable manufacturing
The Pannoramic DESK is an entry-level half-automatic scanner with small footprint and dimensions,
low maintenance, simple and easy use. Optimal for those customers, who want to begin with
digitizing of their tissue samples and intend to use the scanner not for batch processing
(recommended daily scan quantity up to 10 slides).
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Pannoramic DESK 1.20 User’s Guide 1 Product Description
1.1.3 Warning and Information Labels
The following figure contains the labels used on the Pannoramic DESK main unit and the external
mains power supply unit.
Figure 1 – Warning and information labels
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Pannoramic DESK 1.20 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 the base unit
1. Protective cover
2. Protection rail
3. Scan camera
4. Sliding door
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Pannoramic DESK 1.20 User’s Guide 1 Product Description
1.2 System Overview
The standard scope of delivery of the product includes the following hardware and software items.
1.2.1 Pannoramic DESK system
The following figure shows the main components of the Pannoramic DESK system.
Figure 3 – Pannoramic DESK s stem overview
1. 24 V external power supply unit
2. Pannoramic DESK base unit
3. Monitor
4. Mouse
5. Control computer
6. Keyboard
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Pannoramic DESK 1.20 User’s Guide 1 Product Description
1.2.2 Hardware Options
The configuration of the control computer and monitor can vary depending on the product order.
Cameras
Stingray F14 C IRF Medical camera
1 CCD camera for normal brightfield application.
CIS VCC-FC 0FR19CL
CMOS camera for high-quality brightfield
applications allowing fast scanning.
Camera adapters
0.63× adapter 1× adapter 1.6× adapter
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Pannoramic DESK 1.20 User’s Guide 1 Product Description
Warning!
The installation of the cameras in Pannoramic DESK 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 DESK asic Scan Option / Fast Option – base unit equipped with Stingray F146C
IRF or CIS VCC-FC60FR19CL camera for rightfield scanning
Objectives
•Carl Zeiss Plan-Apochromat 20×/NA 0.8
•Carl Zeiss Plan-Apochromat 40× Corr/NA 0.95
Warning!
Do not change correction collar settings on 40×/NA objective, if you
need it to be set, contact customer service.
1.2.3 Control Software
Pannoramic Scanner control software
Optional:
•Extended focus
•Z-stack
•arcode reader (licensed feature)
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Pannoramic DESK 1.20 User’s Guide 1 Product Description
Pannoramic Viewer software (fully functional)
Optional:
•CaseCenter
•Pannoramic Viewer TMA module
•3D Reconstruction module
•QuantCenter, HistoQuant, NuclearQuant, MembraneQuant, and DensitoQuant modules
•Tumor oard module
•E-School Encoder
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Pannoramic DESK 1.20 User’s Guide 2 Installation
2 Installation
Warning!
The installation of Pannoramic DESK 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 4 – Ports on control computer
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Pannoramic DESK 1.20 User’s Guide 2 Installation
1. Status display
2. DVD drive (RW)
3. Power on/off button
4. Earphone and microphone 3.5mm Jack ports
5. 2x US port
6. Power supply connector
7. PS/2 mouse port
8. PS/2 keyboard port
9. 4x US port
10. 2x US port
11. Network port
12. Matrox Solios CameraLink ports (for CIS camera)
13. 1x FireWire port (IEEE 1394 for Stingray F146C camera)
2.2 Connectors and cables
•Control – US cable (between scanner and control computer)
•Preview camera – US cable (between scanner and control computer)
•Stingray – FireWire 1394 cable (between Stingray camera and control computer)
•CIS – a pair of CameraLink cables (between CIS camera and control computer)
•Video cable (between monitor and control computer)
•Power supply cable (between 230V/110V and monitor)
•Power supply cable (between 230V/110V and control computer)
•Power supply cable (between 230V/110V and power supply unit)
•Power supply cable (between 230V/110V and CIS camera)
Warning!
Only connect external devices that are safety extra low voltage rated to
the instrument to avoid the risk of electrical shock.
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