SchapiroLabor/histoCAT external links

---

GitHub - View repository

GitHub.dev - Open in online code editor

Star history - Growth chart over time

deps.dev - Dependencies and security vulnerabilities

Gitingest - Export source code for LLM usage

Repomix - Export source code for LLM usage

uithub - Export source code for LLM usage

Close

SchapiroLabor/histoCAT

Readme badge preview -

If you own this repo, copy the snippet below and add it to your README.md

---

Copy

[![RelatedRepos](https://img.shields.io/badge/related-repos-yellow)](https://relatedrepos.com/gh/SchapiroLabor/histoCAT)

Close

SchapiroLabor / histoCATView on GitHubMore

• External links
• Readme badge

Histology Topography Cytometry Analysis Toolbox

☆69Mar 23, 2026Updated 7 months ago

Alternatives and similar repositories for histoCAT

Users that are interested in histoCAT are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.

• BodenmillerGroup / imctools

  View on GitHub
  Tools to handle IMC data
  ☆25Mar 31, 2022Updated 4 years ago
• camlab-bioml / astir

  View on GitHub
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆59Sep 2, 2026Updated 2 months ago
• BodenmillerGroup / ImcPluginsCP

  View on GitHub
  CellProfiler plugins for multiplexed image analysis
  ☆13Feb 16, 2021Updated 5 years ago
• niaid / sitk-ibex

  View on GitHub
  Aligning images acquired with the IBEX microscopy imaging technique
  ☆20Jun 28, 2026Updated 4 months ago
• miti-consortium / MITI

  View on GitHub
  Minimum Information about Tissue Imaging
  ☆21Oct 18, 2023Updated 3 years ago
• Managed Kubernetes at scale on DigitalOcean • Ad
  DigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
• BodenmillerGroup / ImcSegmentationPipeline

  View on GitHub
  A pixel classification based multiplexed image segmentation pipeline
  ☆108Dec 5, 2023Updated 2 years ago
• akoyabio / phenoptr

  View on GitHub
  Helper functions for working with inForm data.
  ☆25May 3, 2022Updated 4 years ago
• BodenmillerGroup / steinbock

  View on GitHub
  A toolkit for processing multiplexed tissue images
  ☆70Oct 19, 2026Updated 2 weeks ago
• damienArnol / svca

  View on GitHub
  ☆14Jan 16, 2019Updated 7 years ago
• labsyspharm / cylinter

  View on GitHub
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆36Aug 28, 2026Updated 2 months ago
• SunXQlab / ESICCC

  View on GitHub
  ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods
  ☆13Jan 10, 2024Updated 2 years ago
• JinmiaoChenLab / cytofkit

  View on GitHub
  cytofkit: an integrated flow/mass cytometry data analysis pipeline
  ☆61Dec 17, 2020Updated 5 years ago
• walsh-quail-labs / IMC-Lung

  View on GitHub
  ☆24Mar 22, 2023Updated 3 years ago
• hammerlab / cytokit

  View on GitHub
  Microscopy Image Cytometry Toolkit
  ☆118Jul 15, 2022Updated 4 years ago
• Managed hosting for WordPress and PHP on Cloudways • Ad
  Managed hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
• angelolab / ark-analysis

  View on GitHub
  Integrated pipeline for multiplexed image analysis
  ☆110Sep 18, 2026Updated last month
• labsyspharm / mcmicro

  View on GitHub
  Multiple-choice microscopy pipeline
  ☆156Oct 17, 2026Updated 2 weeks ago
• murphygroup / CellSegmentationEvaluator

  View on GitHub
  Evaluating the quality of a cell segmentation method without reference.
  ☆13Jul 26, 2025Updated last year
• qupath / qupath-extension-stardist

  View on GitHub
  QuPath extension to run StarDist nucleus detection
  ☆50Jun 25, 2026Updated 4 months ago
• plevritis-lab / CELESTA

  View on GitHub
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆41May 7, 2024Updated 2 years ago
• BiomedicalMachineLearning / Spacell

  View on GitHub
  ☆30Nov 21, 2019Updated 6 years ago
• nolanlab / TissueSchematics

  View on GitHub
  Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"
  ☆14Mar 3, 2023Updated 3 years ago
• ciccalab / SIMPLI

  View on GitHub
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆38Sep 23, 2025Updated last year
• getzlab / scrinvex

  View on GitHub
  Single Cell RNA Intron-Exon counting
  ☆12May 7, 2020Updated 6 years ago
• Wordpress hosting with auto-scaling - Free Trial Offer • Ad
  Fully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
• pachterlab / kite

  View on GitHub
  kallisto index tag extractor
  ☆20Jul 6, 2019Updated 7 years ago
• klarman-cell-observatory / PowerAnalysisForSpatialOmics

  View on GitHub
  ☆30Oct 4, 2024Updated 2 years ago
• CellProfiling / pipex

  View on GitHub
  A pipeline to transform images into valuable analysis items
  ☆19Sep 21, 2026Updated last month
• MarioniLab / scHOT2019

  View on GitHub
  Instructions and analysis scripts for single cell Higher Order Testing (scHOT)
  ☆10Oct 7, 2020Updated 6 years ago
• ding-lab / morph

  View on GitHub
  ☆16Oct 24, 2025Updated last year
• nolanlab / NeighborhoodCoordination

  View on GitHub
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆77Nov 4, 2024Updated 2 years ago
• ImmuneDynamics / Spectre

  View on GitHub
  A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.
  ☆71Sep 19, 2025Updated last year
• nolanlab / SpatialScore

  View on GitHub
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆16Sep 26, 2021Updated 5 years ago
• nf-core / imcyto

  View on GitHub
  Image Mass Cytometry analysis pipeline
  ☆26Jun 3, 2025Updated last year
• Managed Kubernetes at scale on DigitalOcean • Ad
  DigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
• ionpath / mibilib

  View on GitHub
  Python client for IONpath MIBItracker API, plus utility functions for working with MIBItiff images.
  ☆14Oct 15, 2024Updated 2 years ago
• qupath / models

  View on GitHub
  Trained models for use with QuPath
  ☆16Jun 25, 2026Updated 4 months ago
• CellProfiler / stitching

  View on GitHub
  Image stitching
  ☆13Dec 23, 2018Updated 7 years ago
• niaid / imaris_extensions

  View on GitHub
  Algorithmic and Utility Extensions for the Imaris Program
  ☆21Aug 28, 2026Updated 2 months ago
• vanvalenlab / intro-to-deepcell

  View on GitHub
  An introduction to deepcell and deep learning
  ☆155Oct 21, 2024Updated 2 years ago
• schienstockd / cecelia-legacy

  View on GitHub
  Framework for image and flow cytometry analysis
  ☆33Mar 17, 2026Updated 7 months ago
• saramcardle / Image-Analysis-Scripts

  View on GitHub
  Various scripts written for image analysis utilities
  ☆12Oct 3, 2025Updated last year