Software Support
Software Support
CODEX Software Updates
CODEX® Software Suite
CODEX® workflow makes use of a Software Suite composed of three different programs. This suite is intended to provide a comprehensive solution to the user needs, managing everything from data acquisition to image analysis and interpretation of cytometric data.
The CODEX Instrument Manager controls the fluidics of the CODEX instrument, the integration, and synchronization with companion microscopes, CODEX data formatting, and data transfer.
CIM Instructions
CODEX® Processor is a user-friendly, desktop Java application that prepares CODEX® images for downstream data analysis.
CODEX Processor instructions
The Multiple Analysis Viewer is a tool that allows the visualization and analysis of CODEX images, segmented cells and their sub-populations (or phenotypes). It also allows performing gating and clustering of single cells through X-shift, a population finding algorithm for single-cell multidimensional data.
MAV instructions
Phenoptics Software Updates
inForm 2.6 is an update for inForm 2.1 and later; it can be installed and run without an updated license. Customers with version 2.0 or earlier must upgrade their license in order to run inForm 2.6. Please contact your Akoya Sales Representative for purchasing details.
To install:
1. Download and unzip R installation (version R 3.1.0)
2. Double click on install_R_and_packages.bat
Please Note: R 3.1.0 only needs to be installed the first time inForm is installed on a computer
3. Download and install inForm Setup
inForm 2.6* Setup Files
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R-installation Package (first time installation only)
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User Guides
inForm 2.6 User Manual (PDF)
Release Notes
inForm 2.6 Release Notes (PDF)
inForm 2.6 What’s New (PDF)
Note: inForm 2.6 is released in support of Mantra, Vectra 3, and Vectra Polaris. It does not support Vectra 2. Current Vectra 2 customers should remain on inForm 2.1.
*Windows 10, 64-bit platforms only.
To use phenoptrReports, please install both phenoptr and phenoptrReports:
- phenoptr provides functions that consolidate and analyze output tables created by Akoya Bioscience’s inForm® software.
- phenoptrReports generates shareable reports and visualizations based on phenoptr output. An easy-to-use, front-end GUI is provided to run phenoptr, removing the need to know R scripting to run phenopr functions.
Setup Files
RStudio
Install R
Rtools (Win)
Xcode (OS)
User Guides
Installation Instructions
phenoptrReports Tutorials
Release Notes
0.2.10 phenoptrReports Changelog
0.2.9 phenoptr Changelog
Note: Both the phenoptr and phenoptrReports packages are updated frequently based on user feedback. Please register for updates to be notified as new versions are released.
Phenochart is a whole slide viewer for slides scanned with Vectra Polaris and Vectra 3. It is free to download
Phenochart 1.1.0 Setup Files
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User Guides
Phenochart 1.1.0 User Manual (PDF)
Release Notes
Phenochart 1.1.0 Release Notes (PDF)
Please contact your Akoya Sales Representative for information about upgrading to Mantra 1.0.5.
User Guides
MantraSnap User Manual
Release Notes
Release Notes (PDF)
What’s New (PDF)
*Windows 10, 64-bit platforms only.
Please contact your Akoya Sales Representative for information about upgrading to Vectra 3.0.7.
User Guides
Vectra User Manual
Release Notes
Release Notes (PDF)
What’s New (PDF)
*Windows 10, 64-bit platforms only.
Please contact your Akoya Sales Representative for information about upgrading to Vectra Polaris 1.0.13.
User Guides
Polaris User Manual
Release Notes
Release Notes (PDF)
What’s New (PDF)
*Windows 10, 64-bit platforms only.