https://github.com/BodenmillerGroup/histoCAT

Histology Topography Cytometry Analysis Toolbox
https://github.com/BodenmillerGroup/histoCAT

Last synced: about 2 months ago
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Histology Topography Cytometry Analysis Toolbox

• Host: GitHub
• URL: https://github.com/BodenmillerGroup/histoCAT
• Owner: BodenmillerGroup
• License: other
• Fork: true (SchapiroLabor/histoCAT)
• Created: 2023-04-27T08:19:34.000Z (about 1 year ago)
• Default Branch: master
• Last Pushed: 2023-04-27T07:55:47.000Z (about 1 year ago)
• Last Synced: 2024-01-10T20:23:07.381Z (6 months ago)
• Homepage: https://bodenmillergroup.github.io/histoCAT/
• Size: 11.4 MB
• Stars: 0
• Watchers: 0
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE_agpl-3.0.txt

Lists

• awesome-cytodata - histoCAT - Toolbox to extract quantitative phenotypic descriptors and contextual information for histology and multiplex imaging. (Software / Genetic Perturbations)
• awesome-single-cell - histoCAT - Histology Topography Cytometry Analysis Toolbox (histoCAT) is a package to visualize and analyse highly multiplexed image cytometry data. [histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data](https://www.nature.com/articles/nmeth.4391) (Web portals, apps, and databases / Interactive visualization and analysis)

README

        
# Welcome

![histoCAT Logo ](histoCAT.png)

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

Cite: 

## 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 .

## Installation

Detailed installation instructions are available in the installation manual at .

## User instructions

We are currently working on the [histoCAT wiki](https://github.com/BodenmillerGroup/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](http://www.bodenmillerlab.org/histoCAT_downloads/Data_52_BreastCancerSamples.zip)

The Nature Methods breast cancer data set (large) as a histoCAT session data can be found here: [Session Data](http://www.bodenmillerlab.org/histoCAT_downloads/histoCAT_sessionResubmission.mat)

All other data associated with the Nature Methods publication can be found here:

[[email protected]](http://www.bodenmillerlab.org/research-2/histocat/)

## 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.