Software Support

Software Support

We’re here to support your multiplexed imaging needs.

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.

CODEX® Instrument Manager

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

CODEX® Processor is a user-friendly, desktop Java application that prepares CODEX® images for downstream data analysis.
CODEX Processor instructions

Multiplex Analysis Viewer (MAV)

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® Tissue Analysis Software

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
Download Now

R-installation Package (first time installation only)
Download Now

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.

phenoptrReports & phenoptr

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 Whole Slide Viewer

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
Download Now

User Guides
Phenochart 1.1.0 User Manual (PDF)

Release Notes
Phenochart 1.1.0 Release Notes (PDF)

Mantra 2

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.

Vectra 3

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.

Vectra Polaris

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.