3D Histech PANNORAMIC MIDI RX 1.0 User manual

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

PANNORAMIC® MIDI 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® MIDI RX system 19
1.2.2 Hardware Options 20
1.2.3 Control Software 22
2Installation 23
2.1 Operation System of the Control Computer 23
2.2 Control Computer Ports 25
2.3 Connectors and Cables 26
2.4 Coupling the Lumencor SOLA unit with the scanner 26
2.5 Coupling the Lumencor Spectra 6 Unit with the Scanner 27
2.6 External Power Supply Unit 28
2.7 Power the Scanner On/Off 28
3Preparing Slides and Trays 29
3.1 Affixing Barcode Stickers to Slides 31
3.2 Inserting and Removing Slides 32
3.3 Inserting and Removing the Tray 33
4Software Description 35
4.1 Starting/Exiting Pannoramic® Scanner Software for Research 35
4.1.1 Starting theControl Software 35

PANNORAMIC® MIDI RX 1.0
CONTENTS
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
4.1.2 Exiting Pannoramic® Scanner Software for Research control software 35
4.2 Main Window Functions 36
4.3 Hotkeys 53
5Scanning Modes and Settings 55
5.1 Brightfield Scanning Mode 55
5.1.1 Profile Settings Panel 56
5.1.2 MicroscopeControl Panel 63
5.1.3 Quick Preview Functions 74
5.1.4 Quick Microscope Functions 74
5.2 Fluorescence Microscope Mode 76
5.2.1 Profile Settings Panel 76
5.2.2 Microscope Control Panel 86
5.2.3 Quick Preview Functions 98
5.2.4 Bottom Menu Bar of the Main Window 101
5.3 Planner Mode 102
5.3.1 General Functions at the Main Menu 102
5.3.2 General Functions at the Tray Menu 105
5.3.3 General Functions at the Slide Menu 105
5.3.4 Slide View with Card 107
5.3.5 Table View Mode 110
5.3.6 Card Collection View Mode 111
5.4 Profile and Preview Overview on the Planner 111
5.5 Progress Features 112
6Settings and Services 113
6.1 Settings 113
6.2 Services 123
7Point Spread Function 132
8Using Profiles 134
9Troubleshooting and Maintenance 136
9.1 Activation of the Control Software 136
9.2 Recovery Functions 141
9.3 Safety Information 141
9.3.1 Cleaning the Device 143
9.3.2 Cleaning the Trays 143

PANNORAMIC® MIDI RX 1.0
CONTENTS
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
9.3.3 Preventive Maintenance 143
9.4 Troubleshooting 143
9.4.1 Fluorescent Applications (Optional) 145
9.5 Maintenance 146
9.5.1 Opening the Protective Covers 146
9.5.2 Removing a Slide 147
9.5.3 Installing and Removing the Filter Module (Fluorescent Option) 148
9.5.4 Transporting Pannoramic® MIDI RX 149
10 Technical Data 151

PANNORAMIC® MIDI 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.;US12/663.537
•P1700279; PCT/HU2018/050030
•P1700483
•P1500394;PCT/HU2016/050039; EP 16840280.8.; US15/756.370
•P0700409; US2008/0306964
•P0800181;PCT/HU2009/000027; EP 09721248.4.
•P0600435;PCT/HU2007/000047;EP 2024772;US12/301.781
•P0600177;PCT/HU2007/000018; EP 1.994.398;US12/281.566
•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 grantedpatents,grantedutility 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 whatevernature (including, but not limited to,
general or specific damage, indirect damage, consequentialdamage or incidental damage,
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® MIDI 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 medicaldevice by theU.S. Food and Drug Administration.
Do not usethis device in close proximity to sources of strong electromagneticradiation (e.g.,
unshielded intentional RF sources),as these may interferewith the proper operation.
Third-party disclaimer
3DHISTECH Ltd. is not liable for damage of whatever nature (including, but not limited to, general
or specificdamage, indirect damage, 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® MIDI RX 1.0
DECLARATION OF CONFORMITY
MAY 13, 2021
6
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Declaration of Conformity
3DHISTECH Ltd. declares that the productPannoramic® MIDI RX slidescanner is designedand
produced with considerationof specified requirements according to theIEC 61326-2-6:2012
standard, and conformsto the directives and otherstandards 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,“Particular requirements for automatic and semi-automaticlaboratory
equipment for analysis andother purposes"
Further informationmaybe obtained from the manufacturer:
3DHISTECH Ltd.
3 Öv Street
1141 Budapest –HUNGARY

PANNORAMIC® MIDI 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 safe and 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 6 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® MIDI RX systemidentified by the relevant article
numbers included in the 3DHISTECH OrderingGuide.

PANNORAMIC® MIDI 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 callyour attentionin this manual:
Example(text in bold)
Words or characters that appear on the screen. Theseinclude 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+S hotkey.
Example (textin 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® MIDI 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 section of this User’s Guide contains information andwarnings of a kind that must be
followed by owner/operator personnel.
Warning and advisorysymbols which are used on the base unit of the Pannoramic® MIDI RX and
in section 1.1.3 Warningand InformationLabels have the following meanings:
Warning!
Disconnect mains plug! Remember to unplug the power cord before you open the
Pannoramic® MIDI RX mainunit for maintenance.
Crush hazard! Thereis crush hazard in themovement area of theslide tray during
operation. Please note that the digitizing process has to be interrupted and the tray moved
via the software to the output position before removing it.
The Pannoramic® MIDI RX, includingany of its original accessory components, shouldnot be
operated in any other way than described in chapter 1.1.1 IntendedUse.
Any of the following notesshould bestrictly observed:
Warning!
If operating the deviceother than specified by the manufacturer,the levelof safety will
decrease.
Warning!
Insert the power cord plugs only into a groundingoutlet. The protective action must not be
rendered ineffective by extension cables without protective conductor. The Pannoramic®
MIDI RX has a built-in protection which must not berendered ineffectiveby extension
cables without protective (earth-ground) conductor.

PANNORAMIC® MIDI RX 1.0
NOTES REGARDING OPERATIONAL SAFETY
MAY 13, 2021
10
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® MIDI 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 3DHISTEC H
Customer Service.
Warning!
Check that your local line voltage is compatible with Pannoramic® MIDI 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® MIDI RX does not include any special facilities to protect from samples
with an etching, potentially infectious, toxic, radioactive, or otherhealth-damagingeffect.
You are under obligation to comply with allcurrently binding legislation, notably,national
accident prevention rules when handling samples of this kind.

PANNORAMIC® MIDI RX 1.0
NOTES REGARDING OPERATIONAL SAFETY
MAY 13, 2021
11
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Warning!
Use of this instrument in a dry environment, especially if syntheticmaterialis present
(syntheticclothing, carpets,etc.) may cause damagingelectrostaticdischargesthat may
causeerroneous results.
Warning!
If a Lumencor SOLA fluorescent illumination unit is used, the corresponding warnings
included in the manufacturer’s operating manual have to be observed.
Warning!
A defective Pannoramic® MIDI RX is not classified as domesticwaste. It must be properly
disposed in accordancewith currently valid legalrequirements.
Warning!
The Pannoramic® MIDI RX 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® MIDI RX is a precision instrumentwhich maysuffera
significant reduction in operationalfunctions or even physicaldestructionfollowing
intervention performed in any nonconformingmanner. If theequipment is used in amanner
not specified by the manufacturer,the protection providedby the equipment maybe
impaired.
Caution!
In the event of any non-conformingtype of use, including non-conforming useof assemblies
or single parts, no liability willbe 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. Allclaims for warranty and warrantyservices willbe nulland void in any such
case.

PANNORAMIC® MIDI RX 1.0
NOTES REGARDING OPERATIONAL SAFETY
MAY 13, 2021
12
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Caution!
Dirt or dust may adversely impact the operatingcapability of the Pannoramic® MIDI RX. For
this reason, measures must be taken to eliminate such influences on a maximum possible
degree. During periods of non-use, the Pannoramic® MIDI RX must be protected with a dust
cover. Check that power is turned off before you put the cover on.
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 identicalwith levelof the original
equipment.
Notice:
Electric power to the Pannoramic® MIDI RX is supplied via an externalmains power supply
unit. It allows for operation at line voltages in the range of 100 V to 24 0 V ±10%, 50/60 Hz,
without any extra facilities required for voltage transformation.
There is no further operator (user) action required in case of residual risks.

PANNORAMIC® MIDI 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® MIDI RX 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 minimizedamage. On
receiving noticeof a fault, the Product Manufacturer willbe under obligationto remove the fault,
at his own option, either by providing adequaterepair 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 unauthorizedintervention into theproduct, 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® MIDI RX. Onlyauthorized
3DHISTECH Service personnelor specifically authorized representatives areallowed to handle
repair work. In case of malfunction contact3DHISTECH ServiceSupport first.

PANNORAMIC® MIDI 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® MIDI RX 1.0
PRODUCT DESCRIPTION
MAY 13, 2021
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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® MIDI RX is designed to digitize biological samples and specimens
(histological sections, typically) using transmittedlight microscopy of fluorescent
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 software component of the PC will highly affect the
functionality of the scanner program.
1.1.2 Features and Benefits
The Pannoramic® MIDI RX equippedwith pco.edge4.2bi camera offers world-class
brightfield and fluorescent wholeslidescanningon up to 50 theoreticalfluorescent
channels using 9 physical fluorescent filter positions.An outstanding0.16 µm/pixel
resolution is achieved with the 40×/0.95NA (equivalent to 61.5× magnification)Plan-
Apochromat objective.
Notice:
The above specified pixel resolution may vary dependingon the selected camera.

PANNORAMIC® MIDI RX 1.0
PRODUCT DESCRIPTION
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Key features of the Pannoramic® MIDI RX scanner are:
•A singlemonochrome camera is used both for Brightfield and Fluorescent scanning.
•LED-based RGB illuminationunit
•Up to 9 freely selectable physical color filters for fluorescence
•High-end fluorescent illumination devices –Lumencor SPECTRA6 or SOLA SM Light
Engine
•Multiband filter support
•FL scanning with a low-noise, back illuminated 16-bit scientific sCMOS pco.edge 4.2bi
camera
•New software-aimedflat-field correctioncompensationmethodto createhomogeneous
slide image
•12-slide automaticloadingand scanning
•Improved permanent autofocus
•Compact and robust device
•Good quality and stablemanufacturing
•3MP camera for barcode reading and preview image
•Image sharpening(for both Fluorescenceand Brightfield) feature to improve the visual
appearanceof digitalslides
•Focus algorithm finds the focus whichis most appealingto thehuman eye.
•Deconvolution algorithm

PANNORAMIC® MIDI 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® MIDI RX mainunit,the
external mains power supply unit,and the Lumencor SOLA illumination unit.
Figure1: Warning and information labels

PANNORAMIC® MIDI RX 1.0
PRODUCT DESCRIPTION
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
1.1.4 Base Unit
The following figure shows the main partsof the base unit.
Figure 2: Main parts of the base unit
1. Protectivecovers
2. Point Grey Grasshopper 3 or pco.edge 4.2 bi camera
Fluorescent option A
3. Lumencor SOLAfiber-coupledilluminationunitwithLumencorillumination adapter and cable
Fluorescent option B
4. Lumencor SPECTRA6 Light Engine fiber-coupledilluminationunit
Notice:
Fluorescent systemscan be usedwith pco.edge4.2bi camera only.

PANNORAMIC® MIDI RX 1.0
PRODUCT DESCRIPTION
MAY 13, 2021
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FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
1.2 System Overview
The standard scope of delivery of theproduct includes the following hardware and
software items.
1.2.1 Pannoramic® MIDI RX system
The following figure shows the main components of the Pannoramic® MIDI RX system.
Figure 3: Pannoramic® MIDI RX system overview
1. Pannoramic®MIDI RXbaseunit
2. 24 V external powersupplyunit forPannoramic®MIDI RX
3. Lumencor SPECTRA6 Light Engine illuminationunit (option)
4. Lumencor SOLASM fiber-coupledilluminationunit(option)
5. External power supplyunitforLumencor SOLASM
6. Slide tray
7. Control computer
8. Keyboard
9. Mouse
10. Monitor