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Histology Topography Cytometry Analysis Toolbox (histoCAT) is a package to visualize and analyse multiplexed image cytometry data interactively.

Cite: https://www.nature.com/articles/nmeth.4391

Getting Started

histoCAT is automatically installed from the web when running the app installer file corresponding to your operating system which is available at https://github.com/BodenmillerGroup/histoCAT/releases.

Windows users must have Visual Studio installed for features like PhenoGraph to function. If it’s not already installed on your computer download it from https://www.visualstudio.com/downloads/.

For further informations read the corresponding manual available at https://github.com/BodenmillerGroup/histoCAT/releases.

Installation

Detailed installation instructions are available in the installation manual at https://github.com/BodenmillerGroup/histoCAT/releases.

User instructions

We are currently working on the histoCAT wiki

For further details please read the corresponding manual available at https://github.com/BodenmillerGroup/histoCAT/releases.

Example datasets

Please find a small example data set with every release at https://github.com/BodenmillerGroup/histoCAT/releases

The Nature Methods breast cancer raw data set (large) can be found here: 52 Breast Cancer Samples

The Nature Methods breast cancer data set (large) as a histoCAT session data can be found here: Session Data

All other data associated with the Nature Methods publication can be found here: histoCAT@BodenmillerLab.org

Using histoCAT from source

Please use MATLAB2014b and load the full histoCAT folder into your MATLAB path. Run histoCAT.m to start histoCAT from source.