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BodenmillerGroup

README.md

Welcome to the Bodenmiller Lab Github

This organization serves the purpose to collect analysis and software repositories associated to our research.

Multiplexed image analysis

General instructions on how to analyse imaging mass cytometry (IMC) data can be found in the IMC data analysis workflow. For general discussions and questions relating to IMC data analysis, please raise an issue here.

The following tools have been developed by the lab to perform multiplexed image analysis:

  • steinbock for containerized image processing and segmentation.
  • readimc for reading raw IMC data.
  • ImcSegmentationPipeline for interactive IMC data processing and segmentation.
  • napari-imc for interactive visualization of IMC raw data in napari.
  • cytomapper for multiplexed image visualization in R.
  • cytoviewer for interactive multiplexed image visualization in R.
  • imcRtools for single-cell and spatial analysis in R.
  • IMCDataAnalysis for a reproducible workflow on multiplexed image downstream analysis in R.
  • imcdatasets for a collection of publicly available IMC datasets in R.

Please open issues in the relevant repositories to file bug reports or feature requests.

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  1. IMCDataAnalysis IMCDataAnalysis Public

    R based workflow for multiplexed imaging data

    HTML 28 12

  2. steinbock steinbock Public

    A toolkit for processing multiplexed tissue images

    Python 51 16

  3. ImcSegmentationPipeline ImcSegmentationPipeline Public template

    A pixel classification based multiplexed image segmentation pipeline

    Jupyter Notebook 85 35

  4. imcRtools imcRtools Public

    An R package for handling and analysing imaging mass cytometry data

    R 22 10

  5. cytomapper cytomapper Public

    R package for visualization of highly multiplexed imaging data

    R 31 9

  6. cytoviewer cytoviewer Public

    An interactive multi-channel image viewer for R

    R 6 1

Repositories

Showing 10 of 88 repositories
  • readimc Public

    Python package for reading imaging mass cytometry (IMC) files

    BodenmillerGroup/readimc’s past year of commit activity
    Python 13 MIT 7 4 1 Updated Dec 23, 2024
  • xtiff Public

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

    BodenmillerGroup/xtiff’s past year of commit activity
    Python 28 MIT 4 4 2 Updated Dec 23, 2024
  • steinbock Public

    A toolkit for processing multiplexed tissue images

    BodenmillerGroup/steinbock’s past year of commit activity
    Python 51 MIT 16 31 (7 issues need help) 3 Updated Dec 23, 2024
  • napping Public

    Control point mapping and coordinate transformation using napari

    BodenmillerGroup/napping’s past year of commit activity
    Python 2 MIT 1 1 1 Updated Dec 23, 2024
  • napari-roi Public

    Select regions of interest (ROIs) using napari

    BodenmillerGroup/napari-roi’s past year of commit activity
    Python 4 MIT 2 3 1 Updated Dec 23, 2024
  • mcd2zarr Public

    Command line tool to convert MCD files to Zarr

    BodenmillerGroup/mcd2zarr’s past year of commit activity
    Python 2 MIT 1 2 1 Updated Dec 23, 2024
  • napari-czifile2 Public

    Carl Zeiss Image (.czi) file support for napari

    BodenmillerGroup/napari-czifile2’s past year of commit activity
    Python 6 MIT 7 0 1 Updated Dec 23, 2024
  • airlab-rs Public

    AirLab backend

    BodenmillerGroup/airlab-rs’s past year of commit activity
    Rust 0 MIT 0 2 0 Updated Dec 2, 2024
  • imcRtools Public

    An R package for handling and analysing imaging mass cytometry data

    BodenmillerGroup/imcRtools’s past year of commit activity
    R 22 10 9 2 Updated Oct 29, 2024
  • CISI-IMC Public
    BodenmillerGroup/CISI-IMC’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Oct 13, 2024
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