Repositories list

• steinbock

  Public
  A toolkit for processing multiplexed tissue images

  Python

  •

  MIT License

  •2020 forks•7070 stars•4040 issues•33 pull requests•Updated May 11, 2026May 11, 2026

• xtiff

  Public
  A tiny Python library for writing multi-channel TIFF stacks.

  Python

  •

  MIT License

  •55 forks•3030 stars•44 issues•22 pull requests•Updated May 11, 2026May 11, 2026

• readimc

  Public
  Python package for reading imaging mass cytometry (IMC) files

  Python

  •

  MIT License

  •99 forks•1919 stars•33 issues•11 pull request•Updated May 11, 2026May 11, 2026

• napping

  Public
  Control point mapping and coordinate transformation using napari

  Python

  •

  MIT License

  •22 forks•22 stars•11 issue•11 pull request•Updated May 11, 2026May 11, 2026

• napari-roi

  Public
  Select regions of interest (ROIs) using napari

  Python

  •

  MIT License

  •33 forks•66 stars•33 issues•11 pull request•Updated May 11, 2026May 11, 2026

• mcd2zarr

  Public
  Command line tool to convert MCD files to Zarr

  ome-zarr-converter

  ome-zarr-converter

  Python

  •

  MIT License

  •11 fork•22 stars•22 issues•11 pull request•Updated May 11, 2026May 11, 2026

• napari-czifile2

  Public
  Carl Zeiss Image (.czi) file support for napari

  Python

  •

  MIT License

  •88 forks•77 stars•11 issue•33 pull requests•Updated May 11, 2026May 11, 2026

• imcRtools

  Public
  An R package for handling and analysing imaging mass cytometry data

  rspatialsingle-cell+ 1

  rspatialsingle-cellimc

  R

  •1414 forks•3131 stars•1111 issues•00 pull requests•Updated May 9, 2026May 9, 2026

• gutenTAG

  Public
  MALDI-IHC processing and analysis repository.

  R

  •00 forks•77 stars•22 issues•11 pull request•Updated May 5, 2026May 5, 2026

• airlab-rs

  Public
  AirLab backend

  Rust

  •

  MIT License

  •00 forks•00 stars•22 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• IMCWorkshop2026

  Public
  IMC Workshop 2026

  HTML

  •

  MIT License

  •11 fork•33 stars•11 issue•00 pull requests•Updated Apr 9, 2026Apr 9, 2026

• IMCDataAnalysis

  Public
  R based workflow for multiplexed imaging data

  bioconductorspatial-analysisimage-analysis+ 1

  bioconductorspatial-analysisimage-analysissingle-cell

  HTML

  •

  MIT License

  •1313 forks•3838 stars•66 issues•22 pull requests•Updated Mar 20, 2026Mar 20, 2026

• HR_IMC

  Public
  Code and workflow for high resolution IMC pipeline

  Python

  •44 forks•33 stars•00 issues•00 pull requests•Updated Mar 16, 2026Mar 16, 2026

• RCC_publication

  Public
  Code repository - Meyer et al. - RCC IMC study

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 20, 2026Feb 20, 2026

• histoCAT

  Public
  Histology Topography Cytometry Analysis Toolbox

  MATLAB

  •

  Other

  •2424 forks•55 stars•00 issues•00 pull requests•Updated Feb 13, 2026Feb 13, 2026

• imcdatasets

  Public
  ExperimentHub collection of imaging mass cytometry datasets

  R

  •

  GNU General Public License v3.0

  •55 forks•1212 stars•44 issues•11 pull request•Updated Jan 9, 2026Jan 9, 2026

• T1D_Publication_Steenbuck-Damond

  Public
  This repository contains all code scripts for the type 1 diabetes study from Steenbuck, Damond et al., 2025. Read the preprint here: https://www.biorxiv.org/co…

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 13, 2025Nov 13, 2025

• TNBC_publication

  Public
  Code repository - Meyer et al. - TNBC IMC study

  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 17, 2025Jul 17, 2025

• cytoviewer

  Public
  An interactive multi-channel image viewer for R

  visualizationrshiny+ 2

  visualizationrshinybioconductorimaging

  R

  •22 forks•77 stars•00 issues•00 pull requests•Updated May 27, 2025May 27, 2025

• cytomapper

  Public
  R package for visualization of highly multiplexed imaging data

  spatial-analysissingle-cellbioimaging+ 1

  spatial-analysissingle-cellbioimagingimaging-mass-cytometry

  R

  •1010 forks•3636 stars•1010 issues•22 pull requests•Updated May 27, 2025May 27, 2025

• CISI-IMC

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 13, 2024Oct 13, 2024

• BCmet_publication_scripts

  Public
  R

  •11 fork•11 star•00 issues•00 pull requests•Updated Aug 29, 2024Aug 29, 2024

• MelanomaIMC

  Public
  check static webpage here:

  R

  •11 fork•00 stars•00 issues•11 pull request•Updated May 20, 2024May 20, 2024

• .github

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Jan 29, 2024Jan 29, 2024

• CellSighter

  Public
  Code for the use of CellSighter in the Bodenmiller Lab

  R

  •1111 forks•11 star•00 issues•00 pull requests•Updated Dec 19, 2023Dec 19, 2023

• IMC_NSCLC_CAF

  Public
  IMC analyis CAFs in NSCLC

  11 fork•33 stars•22 issues•00 pull requests•Updated Dec 13, 2023Dec 13, 2023

• ImcSegmentationPipeline

  Public template
  A pixel classification based multiplexed image segmentation pipeline

  pipelineubuntucellprofiler+ 3

  pipelineubuntucellprofilersegmentationimcpixel-classification

  Jupyter Notebook

  •

  MIT License

  •3737 forks•107107 stars•66 issues•00 pull requests•Updated Dec 5, 2023Dec 5, 2023

• CISI-IMC_publication

  Public
  Scripts for CISI-IMC publication

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 29, 2023Nov 29, 2023

• napari-imc

  Public
  Imaging Mass Cytometry (IMC) file type support for napari

  Python

  •

  MIT License

  •55 forks•1313 stars•99 issues•44 pull requests•Updated Oct 19, 2023Oct 19, 2023

• TestData

  Public
  A central repository to store small datasets for testing purposes

  Shell

  •

  Creative Commons Attribution 4.0 International

  •55 forks•11 star•22 issues•00 pull requests•Updated Sep 26, 2023Sep 26, 2023