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    24 repositories

    • maldi-tools

      Public
      Tools for extracting MALDI TIMS TOF 2 Data
      Python
      •0•1•11•5•Updated Feb 19, 2026Feb 19, 2026

    • publications

      Public
      Code from our publications
      Jupyter Notebook
      •4•16•1•0•Updated Feb 6, 2026Feb 6, 2026

    • toffy

      Public
      Scripts for interacting with and generating data from the commercial MIBIScope
      Jupyter Notebook
      •
      MIT License
      •3•15•12•3•Updated Jan 22, 2026Jan 22, 2026

    • ark-analysis

      Public
      Integrated pipeline for multiplexed image analysis
      pythonmultiplexed-imaging
      Jupyter Notebook
      •
      MIT License
      •31•102•45•11•Updated Jan 7, 2026Jan 7, 2026

    • Nimbus-Inference

      Public
      Python
      •
      MIT License
      •6•33•2•1•Updated Jan 6, 2026Jan 6, 2026

    • Nimbus

      Public
      Python
      •
      Other
      •3•33•0•0•Updated Oct 10, 2025Oct 10, 2025

    • alpineer

      Public
      Toolbox for Multiplexed Imaging
      Python
      •
      MIT License
      •0•0•7•1•Updated Aug 29, 2025Aug 29, 2025

    • mbt

      Public
      MIBI binary file extractor written in Rust with Python Bindings.
      Rust
      •
      MIT License
      •1•0•0•1•Updated Jul 10, 2025Jul 10, 2025

    • TNBC_python_scripts

      Public
      Python
      •0•3•3•1•Updated Jun 13, 2025Jun 13, 2025

    • SpaceCat

      Public
      Generate a spatial catalogue from multiplexed imaging data
      Python
      •
      MIT License
      •1•15•2•0•Updated Jun 12, 2025Jun 12, 2025

    • mibi-bin-tools

      Public
      Tools for extracting TIFF images from mibiscope bin files
      Python
      •
      MIT License
      •3•0•4•1•Updated Feb 27, 2025Feb 27, 2025

    • pici-vitessce

      Public
      Python
      •
      MIT License
      •1•0•0•1•Updated Nov 14, 2024Nov 14, 2024

    • tonic-vitessce

      Public
      TONIC Vitessce Visualizations
      TypeScript
      •
      MIT License
      •1•1•0•1•Updated Sep 3, 2024Sep 3, 2024

    • pyimzML

      Public
      A parser to read .imzML files with python
      Python
      •
      Apache License 2.0
      •20•0•0•0•Updated Jun 26, 2024Jun 26, 2024

    • pyFlowSOM

      Public
      Python implementation of the C-optimized FlowSOM library
      Cython
      •
      Other
      •1•1•1•0•Updated Oct 20, 2023Oct 20, 2023

    • pixie

      Public
      Pixie pipeline described in Liu et al., Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering
      Python
      •
      Other
      •31•12•0•0•Updated Aug 3, 2023Aug 3, 2023

    • AMP

      Public archive
      Augmentable MIBI Pipeline
      Python
      •1•1•0•0•Updated Jul 20, 2023Jul 20, 2023

    • MAUI

      Public archive
      GUI for low-level analysis of MIBI data
      MATLAB
      •
      BSD 3-Clause "New" or "Revised" License
      •4•4•0•0•Updated Jul 20, 2023Jul 20, 2023

    • .github

      Public
      Default community health files
      0•0•0•0•Updated Jan 11, 2023Jan 11, 2023

    • FlowSOM

      Public
      Using self-organizing maps for visualization and interpretation of cytometry data
      R
      •23•0•0•0•Updated Jun 15, 2022Jun 15, 2022

    • MIBIsualization

      Public
      Visualization tools for MIBItiff data.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•0•1•1•Updated Mar 4, 2022Mar 4, 2022

    • MibiPipeline

      Public
      Original scripts for analyzing segmented MIBI data
      0•0•0•0•Updated Oct 18, 2019Oct 18, 2019

    • TNBC

      Public
      Original scripts for Keren et al. 2018 Cell paper
      MATLAB
      •0•0•0•0•Updated Oct 18, 2019Oct 18, 2019

    • MIBIAnalysis

      Public
      Low level analysis for MIBI images
      MATLAB
      •5•0•0•0•Updated Apr 4, 2019Apr 4, 2019