AKOYA Vectra 3 User manual

Vectra 3
Quantitative Pathology Imaging System
User's Manual
®
Vectra 3.0.7
Publication Date: August 27, 2019

Notice
This manual is published byAkoya Biosciences, Inc. The information in this document is subject to change without notice
and should not be construed as a commitment byAkoya Biosciences, Inc. Akoya assumes no responsibilityfor anyerrors
that mayappear in this document. This manual is believed to be complete and accurate at the time of publication. In no
event shall Akoya Biosciences be liable for incidental or consequential damages in connection with or arising from the use
of this manual.
This manual describes system operation using Vectra software.
For more information contact:
Akoya Biosciences, Inc.
100 Campus Drive,6th Floor, Marlborough, MA, 01752, USA
Phone: [phone]
Fax: [phone]
Email: [e-mail]
Email (outside the US): [e-mail]
Web site: http://www.akoyabio.com
This software covered byUS Patent 7,655,898.
Akoya Biosciences is a registered trademark of Akoya Biosciences, Inc.
Microsoft is a trademarks of MicrosoftCorporation in the United States and other countries.
All other trademarkes are te propertyof their respective owners.
© 2019, Akoya Biosciences, Inc. All rights reserved.

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Contents
Table of Contents
1 Preface 5
2 Vectra Overview 8
3 Getting Familiar with Vectra 3.0 11
................................................................................................................................... 123.1 Starting the Vectra 3.0 System
................................................................................................................................... 143.2 Starting the Vectra Software
................................................................................................................................... 153.3 Loading Slides onto the Vectra 3.0 System
........................................................................................................................ 15Loading Slides on the Vectra 3.0, 200-Slide System3.3.1
......................................................................................................................................................... 15Loading Slides into the Slide Loader
......................................................................................................................................................... 16Loading Slides onto the Vectra 3.0, 200-Slide Stage Manually
........................................................................................................................ 17Loading Slides on the Vectra 3.0, 6-Slide Stage3.3.2 ................................................................................................................................... 183.4 Overview of the Vectra Home Page
........................................................................................................................ 18Check Dashboard3.4.1 ........................................................................................................................ 19Edit Protocol3.4.2 ........................................................................................................................ 19Scan Slides3.4.3 ........................................................................................................................ 19Launch Phenochart3.4.4 ........................................................................................................................ 19Gear Menu3.4.5
4 System Dashboard 20
................................................................................................................................... 204.1 Use ofthe Dashboard
................................................................................................................................... 204.2 Set Nominal Focus
................................................................................................................................... 224.3 Reference Images
........................................................................................................................ 22Brightfield Reference Images4.3.1 ........................................................................................................................ 25Fluorescence Reference Images4.3.2
5 Creating and Editing Studies and Protocols 27
................................................................................................................................... 275.1 Study and Protocol Creation
................................................................................................................................... 285.2 Brightfield Studies and Protocols
................................................................................................................................... 315.3 Acquiring Brightfield Sample Regions
................................................................................................................................... 335.4 Fluorescence Studies and Protocols
........................................................................................................................ 33Creating a Fluorescence Protocol5.4.1 ................................................................................................................................... 425.5 Setting Exposure Times for MSI Regions
................................................................................................................................... 445.6 Acquiring Fluorescent Sample Regions
................................................................................................................................... 475.7 Automated MSI Field Selection
6 Performing Whole Slide Scans using Vectra 48

Vectra Help
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................................................................................................................................... 486.1 Whole Slide Scanning on the Vectra 3.0, 6-Slide System
................................................................................................................................... 536.2 Whole Slide Scanning on the Vectra 3.0, 200-Slide System
................................................................................................................................... 566.3 Selecting MSI Fields for Acquisition
........................................................................................................................ 56Using Phenochart to select MSI Fields for acquisition6.3.1 ........................................................................................................................ 56Using Vectra to select MSI Fields for acquisition6.3.2
7 Advanced Automated Workflows 58
8 Hardware Overview and Adjustments 60
................................................................................................................................... 608.1 Hardware Descriptions
................................................................................................................................... 718.2 Eyepiece Adjustment
................................................................................................................................... 728.3 Cleaning the Vectra Hardware
9 System Specifications 73
................................................................................................................................... 739.1 Site and Environmental Requirements
10 Hardware Setup Program 75
11 Frequently Asked Questions 81
12 Troubleshooting 83
13 Appendix A: Supported Slide Formats & Dimensions 86
14 Appendix B: Akoya Biosciences TIFF Specification 88
15 Appendix C: Typical Scan & MSI Field Acquisition Times 94
16 Appendix D: Filter Cube Recommendations when using
Opal Reagents 95
17 Appendix E: Compensation Calculations 96
18 Appendix F: Arc-lamp Fluorescence Illuminator User
Information 97
19 Appendix G: Epi-Filter Wedge Correction 107
20 Appendix H: Software EULA 109
Index 117

Preface 5
1 Preface
About This Manual
This manual describes the use and functionality of the Akoya Biosciences Vectra®3.0 Automated
Quantitative Pathology Imaging System. Operating instructions, functional descriptions,
troubleshooting, illustrations, and other relevant information are contained in this manual.
Design Change Disclaimer
Due to design changes and product improvements, information in this manual is subject to change
without notice. Akoya Biosciences reserves the right to change product design at any time without
notice to anyone, which may subsequently affect the content of this manual. Akoya Biosciences
makes every reasonable effort to ensure that this User’s Manual is up to date and corresponds with
the shipped Vectra 3.0.
Reproduction Disclaimer
This User’s Manual is solely for the use of the owner and operator of the Vectra 3.0. Any
reproduction of this publication in part or in whole without the express written consent of Akoya
Biosciences is strictly prohibited. Neither may this publication be made available for electronic
download without the express written consent of Akoya Biosciences.
Technical Support
If you experience any difficulty operating or maintaining the Vectra 3.0, please contact your Akoya
representative. Office hours are 8:00 a.m. to 8:00 p.m. (Eastern Standard Time), Monday through
Friday.
· Telephone: [phone]
· Fax: [phone]
· Email: [e-mail],
· Email (Outside the US): [e-mail]
· Website: http://www.akoyabio.com
CE Testing and Certification
The Vectra 3.0, 6 Slide Instrument has been tested by an independent CE testing
facility, and bears the appropriate CE mark.
Note: Changes or modifications to this equipment not expressly approved by the party responsible
for compliance could void the user’s authority to operate the equipment.
Remarque: Tout changement ou modification apporté à cet instrument non expressément approuvé
par l’entité responsable de la conformité peut annuler l’autorisation d’opérer l’appareil accordée à
l’utilisateur.

6Vectra Help
Contact Akoya Biosciences Technical Support for more information.
Table of Symbols
The table below contains symbols that identify particularly important information and alert you to the
presence of hazards. These symbols may appear in this manual and/or on the product it describes.
Warning: Read instructions to determine possible hazard.
Caution: Read these operating instructions fully before use, and pay particular
attention to sections containing this symbol.
Warning: Surface may be Hot.
Warning: UV Output.
Danger: Electrical Shock hazard.
AC Input
DC Input
USB Port
WEEE symbol. Do not dispose of as unsorted municipal waste.
Contact your Akoya Biosciences Service Engineer for more information.
Operator and Equipment Safety
It is the responsibility of the purchaser to ensure that all persons who operate the Vectra 3.0 are aware of
the following cautionary statements. As with any scientific instrument, there are important safety
considerations, which are highlighted throughout this User’s Manual.
General CautionaryStatements
READ AND UNDERSTAND THIS USER’S MANUAL BEFORE ATTEMPTING TO OPERATE,
TROUBLESHOOT, OR MAINTAIN THE VECTRA 3.0. READING THIS MANUAL FIRST MAKES IT
EASIER AND SAFER TO OPERATE AND MAINTAIN THE SYSTEM.
· The Vectra system contains moving parts that can cause user injury. Always keep your fingers,
long hair, loose clothing, dangling jewelry, etc., away from all moving parts to avoid personal injury
and possible system damage.
· Use only as specified by the operating instructions. Otherwise, the built-in protections may be
impaired.
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Preface 7
· Do not operate the system if there has been a malfunction of the motorized stage or slide loading
components, as this could lead to equipment damage or physical injury. Contact Akoya
Biosciences for assistance.
· Operate the system on a flat, stable surface.
· Do not drop the Vectra imaging module or any other system components.
· Do not expose the imaging module to prolonged heat above 40°C.
· Do not operate the system in an environment with explosive or flammable gases.
· Do not operate the system in places where it may be splashed with liquid.
· Use only the power supply cord set provided with the Vectra system. If the correct cord set for the
location was not provided, please contact Akoya Biosciences for a replacement. Do not use
power supply cords with inadequate ratings.
· Some cables and adapters supplied with the system have proprietary specifications. Do not
connect components supplied by Akoya Biosciences using unqualified cables or adapters. Doing
so could result in damage, and voids the Warranty. Contact Akoya Biosciences for a replacement
if necessary.
· Use only a properly grounded power outlet when connecting the system to power.
· Place equipment and devices in a manner such that the power switches and disconnecting
devices are accessible at all times.
· Follow the recommended maintenance procedures to help ensure optimal performance.
Caution: Installing, servicing, and moving the Vectra system should be performed by Akoya
Biosciences or PerkinElmer authorized and trained personnel only. Power must be
disconnected from the system before servicing.

8Vectra Help
2 Vectra Overview
The topics in this section of the User’s Manual provide general information about the Vectra®3.0
Automated Quantitative Pathology Imaging System. It is important to read and understand the Operator
and Equipment Safety section before using the system. The Hardware Description provides a
description of each of the hardware components that constitute the Vectra system. If you are imaging
fluorescence slides, please review the Fluorescence Illuminator Safety information so that you are
familiar with the fluorescence illuminator and its safety precautions.
Akoya's Vectra 3.0 is a multi-modal, automated imaging system for scanning tissue sections and
microarrays (TMAs), and acquiring multispectral (MSI) images in regions of interest. It supports
workflows including whole slide scanning, annotation and review, with a simple, intuitive interface. It
includes the following software:
· Vectra: Operator-centric software for performing whole slide scans and acquiring MSI regions of
interest. Vectra runs on the workstation connected to the Vectra 3.0 instrument. It can automatically
select regions for MSI acquisition using inForm®Tissue Finder™ software, for fully automated
operation.
· Phenochart™: Operator-centric whole-slide contextual viewer program for annotating slide scans
performed by Vectra. Regions of interest can be highlighted for review or multispectral acquisition.
Phenochart can also be used to enable automated selection of MSI fields by Vectra with the aid of
inForm Tissue Finder. Phenochart is freely distributed and can be used by multiple users who wish to
view or review slide scans taken by Vectra.
· inForm®Tissue Finder™: Analytical software typically used for tissue classification and training,
phenotypic and protein expression measurements, and data export. It can be run from the same
computer that is controlling the Vectra instrument, or on a separate computer. Additional inForm
software ‘seats’ beyond the two seats that come with each Vectra 3.0 system are available for
purchase.
Vectra 3.0 is part of Akoya’s Phenoptics™ pathology workflow solution, leveraging Akoya’s Opal™
multiplexed fluorescent immunohistochemistry reagent kits and inForm’s spectral analysis and classifier
training capabilities. Vectra and Phenochart operate in tandem, using Vectra for whole slide scanning
and multispectral field acquisition and Phenochart for Viewing and Annotation of the scans. inForm is
used for analysis of the multispectral fields.
Phenochart allows the operators to view the whole slide (zoom, pan, etc.), and make decisions
(annotations) on next steps for the sample. Annotations in Phenochart are also used to record the
workflow actions for each slide scan. Annotations include reviewer requested MSI fields, automated
(inForm) field requests, and reviewer edits, approvals, and rejections. The annotation file is a fully
auditable transaction log.
Vectra 3.0 workflows range from simple two-step procedures (e.g. acquire whole slide scan and review)
to automated acquisition of regions of interest selected by the operator or Vectra 3.0 itself.
As an example, a fluorescence workflow might include the following steps:
· Stain tissue with Akoya Biosciences Opal fluorescent IHC reagents
· Acquire whole slide fluorescent imagery using Vectra
· Review the whole slide imagery with Phenochart, and annotate regions of interest for MSI analysis
· Acquire the MSI regions with Vectra
· Use inForm to phenotype cells and measure protein expression levels in the acquired MSI regions.
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Vectra Overview 9
In projects involving many samples, one can automate the region selection in Phenochart, or in Vectra,
using learn-by-example machine learning based on training by an expert operator.
Two Vectra 3.0 models are available: a 6-slide model and 200-slide model, both of which incorporate
automated microscope slide stages. The 6-slide Vectra 3.0 automatically scans up to six slides at a
time. The 200-slide model accepts up to four 50-slide cassettes and automates slide handling to enable
walkaway scanning of up to 200 slides at a time.
Figure 1. Vectra 3.0, 200-Slide Imaging System
Figure 2. Vectra 3.0, 6-Slide Imaging System
The system is for Research Use Only and not for use in diagnostic procedures.

10 Vectra Help
Examples of Vectra Applications
· Whole slide scanning of tissue samples stained with H&E and conventional IHC stains
· Whole slide scanning and multispectral interrogation of tissue samples stained with Akoya
Biosciences Opal™ reagents and markers related to cancer immunology such as CD4, CD8, CD20,
PD-1, PD-L1, cytokeratin
· Simultaneous imaging of IHC staining of p21, p27 and Ki67 in psoriatic skin sections
· Imaging of DAPI, Ki67, CD3, CD20, IgD and CD68 labeled with QDot®probes in lymph node germinal
center
· Multicolor staining of ER, PR, HER1 and HER2 and hematoxylin in a single breast tissue section
· Co-localization analysis of D2-40, SMA, CD34 and CD105 in tonsil sections
· Simultaneous analysis of distribution of CD3, CD1, cytokeratin and hematoxylin in metastatic lymph
nodes
· Automatic identification and analysis of necrosis in liver tissues
· Automatic identification and counting of mitoses
· Multicolor staining of hematoxylin and Schiff’s reagent in glomerular tufts of kidney
· Multicolor staining of DNA with DAPI smooth muscle-myosin heavy chain (SM-MHC) with Cy2
· Smooth muscle α-actin (SMA) with Cy®3 in muscles