Repositories list

• steinbock

  Public
  A toolkit for processing multiplexed tissue images

  Python

  •

  MIT License

  •20•67•38•4•Updated Mar 16, 2026Mar 16, 2026

• readimc

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

  Python

  •

  MIT License

  •9•18•3•1•Updated Mar 16, 2026Mar 16, 2026

• xtiff

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

  Python

  •

  MIT License

  •4•30•4•2•Updated Mar 16, 2026Mar 16, 2026

• napping

  Public
  Control point mapping and coordinate transformation using napari

  Python

  •

  MIT License

  •2•2•1•1•Updated Mar 16, 2026Mar 16, 2026

• napari-roi

  Public
  Select regions of interest (ROIs) using napari

  Python

  •

  MIT License

  •3•6•3•1•Updated Mar 16, 2026Mar 16, 2026

• napari-czifile2

  Public

  BodenmillerGroup/napari-czifile2’s past year of commit activity
  Carl Zeiss Image (.czi) file support for napari

  Python

  •

  MIT License

  •8•7•0•2•Updated Mar 16, 2026Mar 16, 2026

• mcd2zarr

  Public
  Command line tool to convert MCD files to Zarr

  ome-zarr-converter

  ome-zarr-converter

  Python

  •

  MIT License

  •1•2•2•1•Updated Mar 16, 2026Mar 16, 2026

• HR_IMC

  Public
  Code and workflow for high resolution IMC pipeline

  Python

  •4•4•0•0•Updated Mar 16, 2026Mar 16, 2026

• IMCDataAnalysis

  Public

  BodenmillerGroup/IMCDataAnalysis’s past year of commit activity
  R based workflow for multiplexed imaging data

  bioconductorspatial-analysisimage-analysis+ 1

  bioconductorspatial-analysisimage-analysissingle-cell

  HTML

  •

  MIT License

  •13•36•5•2•Updated Feb 23, 2026Feb 23, 2026

• RCC_publication

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

  Jupyter Notebook

  •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

• histoCAT

  Public
  Histology Topography Cytometry Analysis Toolbox

  MATLAB

  •

  Other

  •24•4•0•0•Updated Feb 13, 2026Feb 13, 2026

• imcdatasets

  Public
  ExperimentHub collection of imaging mass cytometry datasets

  R

  •

  GNU General Public License v3.0

  •4•9•4•1•Updated Jan 9, 2026Jan 9, 2026

• imcRtools

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

  rspatialsingle-cell+ 1

  rspatialsingle-cellimc

  R

  •14•30•11•0•Updated Jan 6, 2026Jan 6, 2026

• T1D_Publication_Steenbuck-Damond

  Public

  BodenmillerGroup/T1D_Publication_Steenbuck-Damond’s past year of commit activity
  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

  •0•0•0•0•Updated Nov 13, 2025Nov 13, 2025

• TNBC_publication

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

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Jul 17, 2025Jul 17, 2025

• cytoviewer

  Public
  An interactive multi-channel image viewer for R

  visualizationrshiny+ 2

  visualizationrshinybioconductorimaging

  R

  •2•7•0•0•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

  •10•34•10•2•Updated May 27, 2025May 27, 2025

• airlab-rs

  Public
  AirLab backend

  Rust

  •

  MIT License

  •0•0•2•0•Updated Mar 3, 2025Mar 3, 2025

• CISI-IMC

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Oct 13, 2024Oct 13, 2024

• BCmet_publication_scripts

  Public
  R

  •1•1•0•0•Updated Aug 29, 2024Aug 29, 2024

• MelanomaIMC

  Public
  check static webpage here:

  R

  •1•0•0•1•Updated May 20, 2024May 20, 2024

• .github

  Public
  0•0•0•0•Updated Jan 29, 2024Jan 29, 2024

• CellSighter

  Public
  Code for the use of CellSighter in the Bodenmiller Lab

  R

  •10•1•0•0•Updated Dec 19, 2023Dec 19, 2023

• IMC_NSCLC_CAF

  Public
  IMC analyis CAFs in NSCLC

  1•3•2•0•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

  •37•106•6•0•Updated Dec 5, 2023Dec 5, 2023

• CISI-IMC_publication

  Public
  Scripts for CISI-IMC publication

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 29, 2023Nov 29, 2023

• napari-imc

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

  Python

  •

  MIT License

  •4•12•9•3•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

  •5•1•2•0•Updated Sep 26, 2023Sep 26, 2023

• demos

  Public
  Repository containing demonstrations of lab software

  demobioconductor

  demobioconductor

  1•5•0•0•Updated Sep 14, 2023Sep 14, 2023

• MEZ_XRF

  Public
  This is the repository companion to the MEZ-XRF paper

  Jupyter Notebook

  •0•1•0•0•Updated Aug 31, 2023Aug 31, 2023