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    87 repositories

    • readimc

      Public
      Python package for reading imaging mass cytometry (IMC) files
      Python
      •
      MIT License
      •7•12•3•1•Updated Nov 25, 2024Nov 25, 2024

    • imcRtools

      Public
      An R package for handling and analysing imaging mass cytometry data
      spatialimcrsingle-cell
      R
      •10•22•8•2•Updated Oct 29, 2024Oct 29, 2024

    • xtiff

      Public
      A tiny Python library for writing multi-channel TIFF stacks.
      Python
      •
      MIT License
      •3•28•2•1•Updated Oct 28, 2024Oct 28, 2024

    • steinbock

      Public
      A toolkit for processing multiplexed tissue images
      Python
      •
      MIT License
      •16•50•29•3•Updated Oct 28, 2024Oct 28, 2024

    • napping

      Public
      Control point mapping and coordinate transformation using napari
      Python
      •
      MIT License
      •1•2•1•1•Updated Oct 28, 2024Oct 28, 2024

    • napari-roi

      Public
      Select regions of interest (ROIs) using napari
      Python
      •
      MIT License
      •2•4•3•1•Updated Oct 28, 2024Oct 28, 2024

    • napari-czifile2

      Public
      Carl Zeiss Image (.czi) file support for napari
      Python
      •
      MIT License
      •7•6•0•1•Updated Oct 28, 2024Oct 28, 2024

    • mcd2zarr

      Public
      Command line tool to convert MCD files to Zarr
      ome-zarr-converter
      Python
      •
      MIT License
      •1•2•2•1•Updated Oct 28, 2024Oct 28, 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
      •0•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • cytomapper

      Public
      R package for visualization of highly multiplexed imaging data
      spatial-analysisbioimagingimaging-mass-cytometrysingle-cell
      R
      •9•31•9•2•Updated Jun 25, 2024Jun 25, 2024

    • cytoviewer

      Public
      An interactive multi-channel image viewer for R
      bioconductorimagingvisualizationrshiny
      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-analysissingle-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
      pipelineubuntucellprofilerimcpixel-classificationsegmentation
      Jupyter Notebook
      •
      MIT License
      •36•85•5•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
      •6•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.
      pythonbioinformaticsvuedata-visualizationtoolboxscientificsegmentationsingle-cellcytometryimc
      Vue
      •
      MIT License
      •11•8•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

    • napari-networkx

      Public archive
      A napari plugin to read and write spatial graphs using networkx
      Python
      •
      MIT License
      •1•1•0•0•Updated Feb 17, 2023Feb 17, 2023