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


Getting Started

histoCAT is automatically installed from the web when running the app installer file corresponding to your operating system which is available at

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

For further informations read the corresponding manual available at


Detailed installation instructions are available in the installation manual at

User instructions

We are currently working on the histoCAT wiki

For further details please read the corresponding manual available at

Example datasets

Please find a small example data set with every release at

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:

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.