3D Histech PANNORAMIC SCAN RX User manual

PANNORAMIC® SCAN RX
1.0
USER’S GUIDE
FOR RESEARCH USE ONLY. NOT FORUSE IN DIAGNOSTIC PROCEDURES.
May 13, 2021 –Rev.1

PANNORAMIC® SCAN RX 1.0
CONTENTS
MAY 13, 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® SCANRX 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 SM 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 1.0
CONTENTS
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
4.1.1 Starting theControl Software 36
4.1.2 Exiting Pannoramic® Scanner Software for Research control software 36
4.2 Main Window Functions 37
4.3 Hotkeys 55
5Scanning Modes and Settings 56
5.1 Brightfield Scanning Mode 56
5.1.1 Profile Settings Panel 57
5.1.2 Microscope Control Panel 64
5.1.3 Quick Preview Functions 75
5.1.4 Quick Microscope Functions 75
5.2 Fluorescence Microscope Mode 77
5.2.1 Profile Settings Panel 77
5.2.2 MicroscopeControl Panel 87
5.2.3 Hidden Functions 99
5.2.4 Quick Microscope Functions 100
5.2.5 Bottom Menu Bar of the Main Window 102
5.3 Planner Mode 103
5.3.1 General Functions at the Main Menu 103
5.3.2 General Functions at the Magazine Menu 106
5.3.3 General Functions at the Slide Menu 106
5.3.4 Slide View with Card 108
5.3.5 Table View Mode 110
5.3.6 Card Collection View Mode 111
5.4 Profile and Preview Overview on the Planner 112
5.5 Progress Features 113
6Settings and Services 114
6.1 Settings 114
6.2 Services 125
7Point Spread Function 134
8Using Profiles 136
9Troubleshooting and Maintenance 138
9.1 Activation of the Control Software 138
9.2 Recovery Functions 143
9.3 Safety Information 143

PANNORAMIC® SCAN RX 1.0
CONTENTS
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
9.3.1 Cleaning the Device 144
9.3.2 Cleaning the Magazines 145
9.3.3 Preventive Maintenance 145
9.4 Troubleshooting 145
9.4.1 Fluorescent Applications (Optional) 147
9.5 Maintenance 148
9.5.1 Removing the Protective Covers 148
9.5.2 Removing a Slide 149
9.5.3 Installing and Removing the Filter Module (Fluorescent Option) 151
9.5.4 Removing the Magazine from the Transporting System 153
9.5.5 Transporting Pannoramic® SCANRX 154
10 Technical Data 156

PANNORAMIC® SCAN RX 1.0
DISCLAIMER
MAY 13, 2021
4
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Disclaimer
Copyright © 2001-20213DHISTECH 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; US2008/0306964
•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; US7.663.078
•P0301911; PCT/HU04/00019;EP 1644767; US 7327515
The above mentioned granted patents, granted utilitymodel, registeredtrademarks,pending
internationaland national patent applications and the othercorresponding 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 specificdamage, indirectdamage, consequentialdamageorincidentaldamage,
includingthe results of the analysis of the digitizedslides, forexample, change of health status
related to erroneous diagnosis from the digitized slide(s)) that stems from oris associated with
use of Product, digitized slides, quality of staining,quality of stainedslides, qualityof used
method of staining.3DHISTECHLtd. assumesno responsibility forthe functionalityand fault-
free condition of your “application programs” (Workflows, VBA macros, Commander scripts).

PANNORAMIC® SCAN RX 1.0
DISCLAIMER
MAY 13, 2021
5
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
CAUTION
For Research Use Only. Not for use in diagnosticprocedures. This product has not been approved
or cleared as a medical device by theU.S. Food and Drug Administration.
Do not use this devicein close proximity to sources of strong electromagneticradiation (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 specificdamage, indirectdamage, consequentialdamage or incidentaldamage,including
damage resulting fromlost profits, interruptionof business,loss of business information,
pecuniary loss or similar damage) that stems fromor 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,
IMPLIEDOR OTHERWISE, INCLUDING WITHOUTLIMITATION, ANY WARRANTY OF
MERCHANTABILITY OR FITNESS FOR A PARTICULARPURPOSE.
FurtherInformation
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 1.0
DECLARATION OF CONFORMITY
MAY 13, 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® SCANRX slide scanner is designedand
produced with considerationof 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-automaticlaboratory
equipment for analysis andother purposes”
There is no further operator (user) action required in case of residual risks.
Further informationmay be obtained from the manufacturer:
3DHISTECH Ltd.
3 Öv Street
1141 Budapest –HUNGARY

PANNORAMIC® SCAN RX 1.0
ABOUT THIS USER'S GUIDE
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
About this User's Guide
The purposeof this manual is to assist the user in the safeand reliable operation of the product
described. Before operating thedevice, you must carefully read this instructionmanual, and
adhereto all WARNING and CAUTION notices (refer to chapter Notes RegardingOperational
Safety for more information), anda copy should be kept in the close to the scanner for reference
whenever required.
This User's Guide is a part of the Pannoramic® SCANRX system identified by the relevant article
numbers included in the 3DHISTECH OrderingGuide.

PANNORAMIC® SCAN RX 1.0
CHARACTER FORMATS AND SYMBOLS
MAY 13, 2021
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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 attentionin this manual:
Example (text in bold)
Words or charactersthat appear on thescreen. These include field names, screen and window
titles, push-buttonand menu names, paths or options.Keys on the keyboard.For example,
function keys (such as F11) or the Ctrl+Shotkey.
Example (text in bold and italics)
Cross-references withinthis document or to other documents.
Warning!
It might cause irreversible damage or harmto 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 1.0
NOTES REGARDING OPERATIONAL SAFETY
MAY 13, 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 advisorysymbols which are used on thebase unit of thePannoramic® SCANRX and
in chapter 1.1.3 Warning and InformationLabels havethefollowingmeanings:
Warning!
Disconnect mains plug! Remember to unplugthe power cord before you open the
Pannoramic® SCANRX main unit for maintenance.
Crush hazard! Thereis crush hazard in the movementarea of the slideinsert during
operation. Makesure not to reach with your hands into theinstrument to avoid the risk of
crushing your fingers. Please notethat thedigitizing process has to be interrupted and the
slide magazine moved via software to the output positionbefore removing it.
The Pannoramic® SCANRX, including anyof its originalaccessory components, should not be
operated in any other way than described in chapter1.1.1 IntendedUse.
Any of the following notesshould be strictly observed:
Warning!
If operating the device other than specified by the manufacturer,the levelof 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®
SCANRX has a built-in protection which mustnot berendered ineffectiveby extension
cables without protective (earth-ground) conductor.

PANNORAMIC® SCAN RX 1.0
NOTES REGARDING OPERATIONAL SAFETY
MAY 13, 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, youshouldcontact 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-damagingeffect.
You are under obligation to comply with allcurrently binding legislation, notably,national
accident prevention rules when handling samples of this kind.

PANNORAMIC® SCAN RX 1.0
NOTES REGARDING OPERATIONAL SAFETY
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Warning!
If a Lumencor SOLA SM fluorescent illumination unit is used, the correspondingwarnings
included in the manufacturer’s operating manual have to be observed.
Warning!
A defective Pannoramic® SCANRX is not classified as domestic waste. It must be properly
disposed in accordancewith currently valid legal requirements.
Warning!
The Pannoramic® SCANRX may not beoperated 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® SCANRX is aprecision instrument whichmay suffer a
significant reduction in operationalfunctions or even physical destructionfollowing
intervention performed in any nonconformingmanner.
Caution!
In the event of any non-conformingtype of use, including non-conforming use of assemblies
or single parts, no liability willbe assumed by the Manufacturer. This shallalso apply to
service or repair work of any kind, which is performed by other than authorized service
personnel. Allclaims for warranty and warrantyservices willbe nulland 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 betaken to eliminate such influences on a maximum possible
degree. During periods of non-use, the Pannoramic® SCANRX must beprotected with a
dust cover. Check that power is turned off before you put the cover on .

PANNORAMIC® SCAN RX 1.0
NOTES REGARDING OPERATIONAL SAFETY
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Caution!
Do not position the equipmentso that it is difficult to operate and to disconnect the device
if necessary.
Notice:
The safety level of the equipment afterservicing willbe identical with levelof theoriginal
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 1.0
NOTES ON WARRANTY
MAY 13, 2021
13
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Notes on Warranty
3DHISTECH Ltd. –as the Product Manufacturer –warrantsthe Pannoramic® SCANRX to be free
from faults in material and workmanship at the moment of installation.Defects must be notified
immediately on identificationand maximum effortsmust be undertaken to minimize the amount
of damage as smallas possible. On receiving notice of a fault, the ProductManufacturerwillbe
under obligation to remove the fault, at his own option,either by providing adequate repair
services or by delivering a faultless productfor replacement. No warrantywillbeaccepted in
cases of natural wear (notably, wear and tear parts) or improperproduct handling.
The Product Manufacturer will refuse any liability in the event of damage resulting from faulty
operation, negligence, or unauthorizedintervention into the product, notably, fromthe
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 anykind of maintenanceor repair work at the Pannoramic® SCAN RX. Only
3DHISTECH Service personnelor specifically authorized representatives areallowed to handle
repair work. In case of malfunction, contact the 3DHISTECH ServiceSupport first.

PANNORAMIC® SCAN RX 1.0
TERMS AND ABBREVIATIONS
MAY 13, 2021
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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 1.0
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 digitizebiologicalsamples and specimens
(histological sections, typically) using transmittedlight 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
becauseof information loss.
Warning!
Any modificationto a hardware or softwarecomponent of thePC will highly affectthe
functionality of the scanner program.
1.1.2 Features and Benefits
The Pannoramic® SCANRX offers world class brightfieldand fluorescent whole slide
scanning on up to 50 virtual fluorescent channels using 9 physicalfluorescentfilter
positions. An outstanding 0.12 µm/pixel(in Brightfield) and 0.16µm/pixel (in Fluorescent)
resolution is achieved with the 40×/NA 0.95 (equivalent to 80× magnificationin BF and 62×
magnification in FL) Plan-Apochromat objective.
Key features of the Pannoramic® SCAN RX Scanner are:
•A singlemonochrome camera is used for both Brightfield and Fluorescent scanning.
•LED-based RGB illuminationunit
•Up to 9 freely selectable physicalcolor 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
•Software-aimed flat-field correction compensation method to create homogeneous slide
image

PANNORAMIC® SCAN RX 1.0
PRODUCT DESCRIPTION
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
•150-slideautomaticloadingand scanning
•Improved permanent autofocus
•3MP camera for barcode reading and preview image
•Image sharpening(both for Fluorescenceand Brightfield) feature whichimprove the
visual appearanceof digitalslides
•Focus algorithm finds the focus whichis most appealingto thehuman eye
•Deconvolution algorithm
•Compact and robust device
•Good quality and stablemanufacturing
Pannoramic® SCANRX is an optimal choice for customers who need highqualitydaily
throughput grantedby the loading capacityof 150 slides.

PANNORAMIC® SCAN RX 1.0
PRODUCT DESCRIPTION
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
1.1.3 Warning and InformationLabels
The following figure contains the labels used on thePannoramic® SCANRX mainunit, the
external mains power supply unit,and the Lumencor SOLA SM illumination unit.
Figure1: Warning and information labels

PANNORAMIC® SCAN RX 1.0
PRODUCT DESCRIPTION
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Notice:
The symbolat thefeeder area calls attention to bio-hazardous materials in use.
1.1.4 Base Unit
The following figure shows the main partsof the base unit.
Figure 2. Main parts of the base unit
1. Protectivecover
2. Output stack for magazines
3. Input stack for magazines
4. Protective cover for magazine loader
5. Magazine feeder door/cover
6. Point Grey Grasshopper3 or pco.edge 4.2 bi camera
7. Protective rails
Fluorescent option A
8. Lumencor SOLA SM fiber-coupledillumination unit
9. Lumencor illumination adapter
10. Lumencor illumination cable

PANNORAMIC® SCAN RX 1.0
PRODUCT DESCRIPTION
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
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 hardwareand
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
1. Lumencor SOLASM fiber-coupledilluminationunit(optional)
2. 24 V externalpowersupplyunit