3D Histech PANNORAMIC SCAN RX 1.1 User manual

PANNORAMIC® SCAN RX
1.1
USER’S GUIDE
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
November 18, 2021 –Rev.1

PANNORAMIC® SCAN RX 1.1
CONTENTS
NOVEMBER 18, 2021
1
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Contents
Contents 1
Disclaimer 4
Declaration of Conformity 6
About this User's Guide 7
Character Formats and Symbols 8
Notes Regarding Operational Safety 9
Notes on Warranty 13
Terms and Abbreviations 14
1Product Description 15
1.1 Product overview 15
1.1.1 Intended use 15
1.1.2 Features and benefits 15
1.1.3 Warning and information labels 17
1.1.4 Base unit 18
1.2 System overview 19
1.2.1 Pannoramic® SCAN RX system 19
1.2.2 Hardware options 20
1.2.3 Control software 22
2Installation 24
2.1 Operation system of the control computer 24
2.2 Control computer ports 26
2.3 Connectors and cables 27
2.4 Coupling the Lumencor SOLA U-NIR unit with the scanner 28
2.5 Coupling the Lumencor Spectra 6 unit with the scanner 28
2.6 External power supply unit 29
2.7 Power the scanner on/off 29
3Operating Slides and Magazines 30
3.1 Preparing slides and magazines 30
3.2 Affixing barcode stickers to slides 32
3.3 Inserting and removing slides 33
4Software Description 36
4.1 Starting/exiting Pannoramic® Scanner Software for Research 36

PANNORAMIC® SCAN RX 1.1
CONTENTS
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
4.1.1 Starting the control software 36
4.1.2 Exiting Pannoramic® Scanner Software for Research control software 36
4.2 Main window functions 37
4.3 Hotkeys 56
5Scanning Modes and Settings 57
5.1 Brightfield scanning mode 57
5.1.1 Profile settings panel 58
5.1.2 Microscope control panel 65
5.1.3 Quick preview functions 77
5.1.4 Quick microscope functions 77
5.2 Fluorescence microscope mode 79
5.2.1 Profile settings panel 79
5.2.2 Microscope control panel 89
5.2.3 Hidden functions 101
5.2.4 Quick microscope functions 102
5.2.5 Bottom menu bar of the main window 104
5.3 Planner mode 105
5.3.1 General functions at the main menu 105
5.3.2 General functions at the magazine menu 108
5.3.3 General functions at the slide menu 108
5.3.4 Slide view with card 110
5.3.5 Table view mode 112
5.3.6 Card collection view mode 113
5.4 Profile and preview overview on the planner 114
5.5 Progress features 115
6Settings and Services 116
6.1 Settings 116
6.2 Services 127
7Point Spread Function 138
8Using Profiles 140
9Troubleshooting and Maintenance 142
9.1 Activation of the control software 142
9.2 Recovery functions 147
9.3 Safety information 147

PANNORAMIC® SCAN RX 1.1
CONTENTS
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
9.3.1 Cleaning the device 149
9.3.2 Cleaning the magazines 149
9.3.3 Preventive maintenance 149
9.4 Troubleshooting 149
9.4.1 Fluorescent applications (optional) 151
9.5 Maintenance 152
9.5.1 Removing the protective covers 152
9.5.2 Removing a slide 153
9.5.3 Installing and removing the filter module (fluorescent option) 155
9.5.4 Removing the magazine from the transporting system 157
9.5.5 Transporting Pannoramic® SCAN RX 158
10 Technical Data 160

PANNORAMIC® SCAN RX 1.1
DISCLAIMER
NOVEMBER 18, 2021
4
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Disclaimer
Copyright © 2001-2021 3DHISTECH Ltd.
All rights reserved.
Intellectual property related to the 3DHISTECH products are as follows:
•P1300124; PCT/HU2014/000020; EP 14745228.8.; US 14/771.380
•P0700404; PCT/HU2008/000065; EP 08762668.5.; US 12/663.537
•P1700279; PCT/HU2018/050030
•P1700483
•P1500394; PCT/HU2016/050039; EP 16840280.8.; US 15/756.370
•P0700409; US 2008/0306964
•P0800181; PCT/HU2009/000027; EP 09721248.4.
•P0600435; PCT/HU2007/000047; EP 2024772; US 12/301.781
•P0600177; PCT/HU2007/000018; EP 1.994.398; US 12/281.566
•P0900741; PCT/HU2010/000130; EP 10812989.1.
•P0900142; PCT/HU2010/000027; EP 10726183.6
•P101036; PCT/IB2005/050351; EP 1789831; US 7.663.078
•P0301911; PCT/HU04/00019; EP 1644767; US 7327515
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).

PANNORAMIC® SCAN RX 1.1
DISCLAIMER
NOVEMBER 18, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
CAUTION
For Research Use Only. Not for use in diagnostic procedures. 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.
Third-party disclaimer
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 a third-party company.
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.
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
3 Öv Street, 1141 Budapest –HUNGARY

PANNORAMIC® SCAN RX 1.1
DECLARATION OF CONFORMITY
NOVEMBER 18, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Declaration of Conformity
3DHISTECH Ltd. declares that the product Pannoramic® SCAN RX slide scanner is designed and
produced with consideration of specified requirements according to the standards listed below:
IEC 61010-1:2010, “Safety Requirements for Electrical Equipment for Measurement, Control, and
Laboratory Use –Part 1: General Requirements”
IEC 61010-2-081:2015, “Safety requirements for electrical equipment for measurement, control and
laboratory use –Part 2-081: Particular requirements for automatic and semi-automatic laboratory
equipment for analysis and other purposes”
There is no further operator (user) action required in case of residual risks.
Further information may be obtained from the manufacturer:
3DHISTECH Ltd.
3 Öv Street
1141 Budapest –HUNGARY

PANNORAMIC® SCAN RX 1.1
ABOUT THIS USER'S GUIDE
NOVEMBER 18, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
About this User's Guide
The purpose of this manual is to assist the user in the safe and reliable operation of the product
described. Before operating the device, you must carefully read this instruction manual, and
adhere to all WARNING and CAUTION notices (refer to chapter Notes Regarding Operational
Safety for more information), and a copy should be kept in the close to the scanner for reference
whenever required.
This User's Guide is a part of the Pannoramic® SCAN RX system identified by the relevant article
numbers included in the 3DHISTECH Ordering Guide.

PANNORAMIC® SCAN RX 1.1
CHARACTER FORMATS AND SYMBOLS
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Character Formats and Symbols
The following character formats and symbols call your attention in this manual:
Example (text in bold)
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+S hotkey.
Example (text in bold and italics)
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.
Notice:
Calls attention to some important features.

PANNORAMIC® SCAN RX 1.1
NOTES REGARDING OPERATIONAL SAFETY
NOVEMBER 18, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Notes Regarding Operational Safety
The below chapter 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® SCAN RX and
in chapter 1.1.3 Warning and Information Labels have the following meanings:
Warning!
Disconnect mains plug! Remember to unplug the power cord before you open the
Pannoramic® SCAN RX main unit for maintenance.
Crush hazard! There is crush hazard in the movement area of the slide insert during
operation. Make sure not to reach with your hands into the instrument to avoid the risk of
crushing your fingers. Please note that the digitizing process has to be interrupted and the
slide magazine moved via software to the output position before removing it.
The Pannoramic® SCAN RX, including any of its original accessory components, should not be
operated in any other way than described in chapter 1.1.1 Intended Use.
Any of the following notes should be strictly observed:
Warning!
If operating the device other than specified by the manufacturer, the level of safety will
decrease.
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®
SCAN RX has a built-in protection which must not be rendered ineffective by extension
cables without protective (earth-ground) conductor.

PANNORAMIC® SCAN RX 1.1
NOTES REGARDING OPERATIONAL SAFETY
NOVEMBER 18, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Warning!
Never operate the device in explosion-risk environment.
Warning!
If protective devices are found to be ineffective, the Pannoramic® SCAN RX 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.
Warning!
Check that your local line voltage is compatible with Pannoramic® SCAN RX specifications
before you turn power on.
Warning!
Only connect external devices to the instrument which are approved to avoid the risk of
electrical shock.
Warning!
The Pannoramic® SCAN RX 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.

PANNORAMIC® SCAN RX 1.1
NOTES REGARDING OPERATIONAL SAFETY
NOVEMBER 18, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Warning!
If a Lumencor SOLA U-NIR fluorescent illumination unit is used, the corresponding warnings
included in the manufacturer’s operating manual have to be observed.
Warning!
A defective Pannoramic® SCAN RX is not classified as domestic waste. It must be properly
disposed in accordance with currently valid legal requirements.
Warning!
The Pannoramic® SCAN RX 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® SCAN RX is a precision instrument which may suffer a
significant reduction in operational functions or even physical destruction following
intervention performed in any nonconforming manner.
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.
Caution!
Dirt or dust may adversely impact the operating capability of the Pannoramic® SCAN RX. For
this reason, measures must be taken to eliminate such influences on a maximum possible
degree. During periods of non-use, the Pannoramic® SCAN RX must be protected with a
dust cover. Check that power is turned off before you put the cover on.

PANNORAMIC® SCAN RX 1.1
NOTES REGARDING OPERATIONAL SAFETY
NOVEMBER 18, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Caution!
Do not position the equipment so that it is difficult to operate and to disconnect the device
if necessary.
Notice:
The safety level of the equipment after servicing will be identical with level of the original
equipment.
Notice:
Electric power to the Pannoramic® SCAN RX 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.

PANNORAMIC® SCAN RX 1.1
NOTES ON WARRANTY
NOVEMBER 18, 2021
13
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Notes on Warranty
3DHISTECH Ltd. –as the Product Manufacturer –warrants the Pannoramic® SCAN RX 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 to minimize 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 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® SCAN RX. Only
3DHISTECH Service personnel or specifically authorized representatives are allowed to handle
repair work. In case of malfunction, contact the 3DHISTECH Service Support first.

PANNORAMIC® SCAN RX 1.1
TERMS AND ABBREVIATIONS
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Terms and Abbreviations
Term
Description
CSV
Comma Separated Value
FOV
Field of View
NA
Numerical Aperture
Photobleaching
A phenomenon that leads to a dramatic loss of fluorescence emission intensity (a
fluorophore permanently loses the ability to fluoresce) due to photon-induced chemical
damage and covalent modification, therefore fluorescent signals cannot be properly
detected.
SWAP
A file that is used as a temporary location on the computer to store information that is not
currently used by the RAM.
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, comment, send it to a colleague electronically for co-operation or advice,
and so on.

PANNORAMIC® SCAN RX 1.1
PRODUCT DESCRIPTION
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
1Product Description
1.1 Product overview
1.1.1 Intended use
The Pannoramic® SCAN RX is designed to digitize biological samples and specimens
(histological sections, typically) using transmitted light microscopy of fluorescence
microscopy techniques.
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 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® SCAN RX offers world class brightfield and fluorescent whole slide
scanning on up to 50 virtual fluorescent channels using 9 physical fluorescent filter
positions. An outstanding 0.12 µm/pixel (in Brightfield) and 0.16 µm/pixel (in Fluorescent)
resolution is achieved with the 40×/NA 0.95 (equivalent to 80× magnification in BF and 62×
magnification in FL) Plan-Apochromat objective.
Key features of the Pannoramic® SCAN RX Scanner are:
•A single monochrome camera is used for both Brightfield and Fluorescent scanning.
•LED-based RGB illumination unit
•Up to 9 freely selectable physical color filters for fluorescence
•High-end fluorescent illumination device –Lumencor SPECTRA 6 Light Engine
•Multiband filter support
•FL scanning with a low-noise, back illuminated 16 bit sCMOS pco.edge 4.2 bi camera

PANNORAMIC® SCAN RX 1.1
PRODUCT DESCRIPTION
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
•Software-aimed flat-field correction compensation method to create homogeneous slide
image
•150-slide automatic loading and scanning
•Improved permanent autofocus
•3MP camera for barcode reading and preview image
•Image sharpening (both for Fluorescence and Brightfield) feature which improve the
visual appearance of digital slides
•Focus algorithm finds the focus which is most appealing to the human eye
•Deconvolution algorithm
•Compact and robust device
•Good quality and stable manufacturing
Pannoramic® SCAN RX is an optimal choice for customers who need high quality daily
throughput granted by the loading capacity of 150 slides.

PANNORAMIC® SCAN RX 1.1
PRODUCT DESCRIPTION
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
1.1.3 Warning and information labels
The following figure contains the labels used on the Pannoramic® SCAN RX main unit, the
external mains power supply unit, and the Lumencor SOLA U-NIR illumination unit.
Figure 1: Warning and information labels

PANNORAMIC® SCAN RX 1.1
PRODUCT DESCRIPTION
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Notice:
The symbol at the feeder area refers to the possibility of exposure to biological hazards
whenever handling slides. This symbol is used as the biohazard label because there is no
appropriate symbol for this biohazard level. The biological hazard is minimal because the
minimally hazardous sample is enclosed between the glass slide and the coverslip.
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. Output stack for magazines
3. Input stack for magazines
4. Protective cover for magazine loader
5. Magazine feeder door/cover
6. Point Grey Grasshopper 3 or pco.edge 4.2 bi camera
7. Protective rails
Fluorescent option A
8. Lumencor SOLA U-NIR fiber-coupled illumination unit

PANNORAMIC® SCAN RX 1.1
PRODUCT DESCRIPTION
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
9. Lumencor illumination adapter
10. Lumencor illumination cable
Fluorescent option B
8. Lumencor SPECTRA 6 Light Engine fiber-coupled illumination unit
9. Lumencor illumination adapter
10. Lumencor illumination cable
1.2 System overview
The standard scope of delivery of the product includes the following hardware and
software components.
1.2.1 Pannoramic® SCAN RX system
The following figure shows the main components of the Pannoramic® SCAN RX system.
Figure 3. Pannoramic® SCAN RX system overview