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    160 repositories

    • multi-dimensional-imaging-and-analysis

      Public
      Jupyter Notebook
      •1•4•0•0•Updated Aug 21, 2025Aug 21, 2025

    • py-bioimage-qc

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 21, 2025Aug 21, 2025

    • Spheroid_culture

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025

    • asf-tools

      Public
      ASF Tools command line tool-kit for ASF operations.
      Python
      •
      MIT License
      •1•0•8•1•Updated Aug 19, 2025Aug 19, 2025

    • introduction-to-image-analysis

      Public
      Jupyter Notebook
      •
      Creative Commons Attribution Share Alike 4.0 International
      •3•3•0•0•Updated Aug 18, 2025Aug 18, 2025

    • IDR-Training-Data

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Aug 17, 2025Aug 17, 2025

    • Imaris-3D-LN-stats

      Public
      Imaris-3D-LN-stats
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

    • cutandrun

      Public
      Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
      Nextflow
      •
      MIT License
      •58•0•0•0•Updated Aug 11, 2025Aug 11, 2025

    • dynamical-systems

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Aug 1, 2025Aug 1, 2025

    • TYPEx

      Public
      Deep cell phenoTYPE characterisation using multipleX imaging
      R
      •
      MIT License
      •0•0•1•0•Updated Aug 1, 2025Aug 1, 2025

    • sparks-ai

      Public template
      HTML
      •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

    • TRACERx-PHLEX

      Public
      Modular pipeline for integrated analysis of the tumour microenvironment using multiplex imaging
      Shell
      •
      MIT License
      •0•13•7•0•Updated Jul 29, 2025Jul 29, 2025

    • hts_neutralisation_launcher

      Public
      Automate neutralisation analyses
      Python
      •1•0•2•0•Updated Jul 25, 2025Jul 25, 2025

    • Image-Analysis-Group

      Public
      We are the Image Analysis Group at the Francis Crick Institute.
      Jupyter Notebook
      •
      Creative Commons Attribution Share Alike 4.0 International
      •2•2•4•0•Updated Jul 24, 2025Jul 24, 2025

    • chronogram

      Public
      cast and annotate metadata, laboratory & clinical data
      R
      •
      Other
      •0•3•0•0•Updated Jul 24, 2025Jul 24, 2025

    • AIoD-Model-Registry

      Public
      The core registry for all AI models available on AI on Demand
      Python
      •0•1•3•1•Updated Jul 24, 2025Jul 24, 2025

    • muvis-align

      Public
      Testing stitching of multiview-stitcher
      Python
      •
      Other
      •0•1•0•0•Updated Jul 21, 2025Jul 21, 2025

    • Segment-Flow

      Public
      Nextflow pipeline for deep learning segmentation models
      Python
      •1•2•0•0•Updated Jul 18, 2025Jul 18, 2025

    • deep-imcyto

      Public
      Nextflow pipeline for IMC segmentation tasks.
      Python
      •
      Other
      •0•4•15•0•Updated Jul 18, 2025Jul 18, 2025

    • bc_matlab

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • ai-on-demand

      Public
      Python
      •
      GNU General Public License v3.0
      •0•1•2•1•Updated Jul 14, 2025Jul 14, 2025

    • OmeSliCC

      Public
      Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)
      ome-zarr-converter
      Python
      •
      Other
      •1•7•0•0•Updated Jul 14, 2025Jul 14, 2025

    • Cell_spot_quant

      Public
      ImageJ Macro
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • bc_jupyter

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • bc_rstudio

      Public
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • napari-mass

      Public
      Microscopy Array Section Setup napari plugin
      Python
      •
      Other
      •0•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • TWOMBLI

      Public
      A ImageJ Plugin implementation of TWOMBLI
      Java
      •
      Creative Commons Attribution 4.0 International
      •5•0•1•1•Updated Jul 4, 2025Jul 4, 2025

    • aiod_utils

      Public
      Python
      •0•0•1•0•Updated Jun 26, 2025Jun 26, 2025

    • Enhancing-Reproducibility

      Public
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •0•4•0•0•Updated Jun 24, 2025Jun 24, 2025

    • bc_desktop

      Public
      [MOVED] Batch Connect - Desktop
      Shell
      •
      MIT License
      •3•0•0•0•Updated Jun 17, 2025Jun 17, 2025