Latest News

We have release histoCAT_1.78.3, which now works on updated Windows and MacOS systems and leverages MATLAB2022b.

For the next major update, we would like to learn more about your individual use cases and current needs.

Please fill out this survey to let us know your opinions: HistoCAT survey

Welcome

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/SchapiroLabor/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/SchapiroLabor/histoCAT/releases.

Installation

Detailed installation instructions are available in the installation manual at https://github.com/SchapiroLabor/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.

Installing the latest cloud build

• Please go to https://github.com/yusufozgur/histoCAT/actions
• click on the latest compile_histoCAT action's run
• At the bottom of the page, you will see artifact's, which are histoCAT builds for the following operating systems: Windows, Linux, MacOS.
• If you are logged in to GitHub, you should be able to download your desired build.
• Download the zip for zour operating system, extract the installer inside. Then run the installer.

For MACOS

If you have histoCAT already installed, delete your previous installation. This could be done through finder or via command line

rm -rf /Applications/histoCAT

Also, during installation, you may encounter error "Apple could not verify histoCAT is free of malware that may harm your Mac or compromise your privacy.". To, fix this, run the following in command line

xattr -d com.apple.quarantine path_to_histoCAT_Installer.app

If you need to run histoCAT from terminal on MacOS, run it using the script while providing Matlab Runtime Path

/Applications/histoCAT/application/run_histoCAT.sh /Applications/MATLAB/MATLAB_Runtime

Using histoCAT from source

• Use MATLAB 2022b, newer versions are not compatible with the codebase.
• Make sure following are installed
  • Image Processing Toolbox
  • Statistics and Machine Learning Toolbox
  • Parallel Computing Toolbox
  • Matlab Compiler (Only if you want to produce compiled installers)
  • Mapping Toolbox
• In the MATLAB IDE, navigate to the root of this repository, make sure you are in histoCAT/ folder and not in the histoCAT/histoCAT/ subfolder
• In the MATLAB IDE, run set_path, this makes sure all functions defined in the .m files in the subfolders are accessible, while excluding compilation folders.
• Run histoCAT to start histoCAT from source.
• Run compile to compile and produce installer for histoCAT.