Repositories list

• readimc

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

  Python

  •

  MIT License

  •7•13•4•1•Updated Dec 23, 2024Dec 23, 2024

• xtiff

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

  Python

  •

  MIT License

  •4•28•4•2•Updated Dec 23, 2024Dec 23, 2024

• steinbock

  Public
  A toolkit for processing multiplexed tissue images

  Python

  •

  MIT License

  •16•51•31•3•Updated Dec 23, 2024Dec 23, 2024

• napping

  Public
  Control point mapping and coordinate transformation using napari

  Python

  •

  MIT License

  •1•2•1•1•Updated Dec 23, 2024Dec 23, 2024

• napari-roi

  Public
  Select regions of interest (ROIs) using napari

  Python

  •

  MIT License

  •2•4•3•1•Updated Dec 23, 2024Dec 23, 2024

• mcd2zarr

  Public
  Command line tool to convert MCD files to Zarr

  ome-zarr-converter

  Python

  •

  MIT License

  •1•2•2•1•Updated Dec 23, 2024Dec 23, 2024

• napari-czifile2

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

  Python

  •

  MIT License

  •7•6•0•1•Updated Dec 23, 2024Dec 23, 2024

• airlab-rs

  Public
  AirLab backend

  Rust

  •

  MIT License

  •0•0•2•0•Updated Dec 2, 2024Dec 2, 2024

• imcRtools

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

  spatialimcr+ 1single-cell

  R

  •10•22•9•2•Updated Oct 29, 2024Oct 29, 2024

• CISI-IMC

  Public
  Jupyter Notebook

  •

  MIT License

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

• TNBC_publication

  Public
  Code repository - TNBC IMC study

  Jupyter Notebook

  •0•0•0•0•Updated Sep 5, 2024Sep 5, 2024

• BCmet_publication_scripts

  Public
  R

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

• cytomapper

  Public
  R package for visualization of highly multiplexed imaging data

  spatial-analysisbioimagingimaging-mass-cytometry+ 1single-cell

  R

  •9•31•9•2•Updated Jun 25, 2024Jun 25, 2024

• cytoviewer

  Public
  An interactive multi-channel image viewer for R

  bioconductorimagingvisualization+ 2rshiny

  R

  •1•6•0•0•Updated Jun 25, 2024Jun 25, 2024

• MelanomaIMC

  Public
  check static webpage here:

  R

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

• imcdatasets

  Public
  ExperimentHub collection of imaging mass cytometry datasets

  R

  •

  GNU General Public License v3.0

  •4•5•3•0•Updated Mar 16, 2024Mar 16, 2024

• IMCDataAnalysis

  Public
  R based workflow for multiplexed imaging data

  bioconductorspatial-analysisimage-analysis+ 1single-cell

  HTML

  •

  MIT License

  •12•28•3•1•Updated Feb 12, 2024Feb 12, 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

  •6•1•0•0•Updated Dec 19, 2023Dec 19, 2023

• IMC_NSCLC_CAF

  Public
  IMC analyis CAFs in NSCLC

  0•2•1•0•Updated Dec 13, 2023Dec 13, 2023

• ImcSegmentationPipeline

  Public template
  A pixel classification based multiplexed image segmentation pipeline

  pipelineubuntucellprofiler+ 3imcpixel-classificationsegmentation

  Jupyter Notebook

  •

  MIT License

  •35•85•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

  •3•9•8•1•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

  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

• histocat-web

  Public
  Histology Topography Cytometry Analysis Toolbox (histoCAT) for Web.

  pythonbioinformaticsvue+ 8data-visualizationtoolboxscientificsegmentationsingle-cellcytometryimc+ 1

  Vue

  •

  MIT License

  •11•7•11•5•Updated Jul 22, 2023Jul 22, 2023

• SABER-IMC_publication

  Public
  MIT License

  •0•1•0•0•Updated May 16, 2023May 16, 2023

• histoCAT

  Public
  Histology Topography Cytometry Analysis Toolbox

  MATLAB

  •

  Other

  •23•1•0•0•Updated Apr 27, 2023Apr 27, 2023

• BC_LN_metastses

  Public
  Jupyter Notebook

  •0•2•0•0•Updated Feb 17, 2023Feb 17, 2023