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    186 repositories

    • muvis-align

      Public
      Testing stitching of multiview-stitcher
      Python
      •
      Other
      •0•1•0•0•Updated Feb 21, 2026Feb 21, 2026

    • spc-data-explorer

      Public
      Dashboard for exploring cell painting data from Cell Profiler & AI/ML models
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 21, 2026Feb 21, 2026

    • lyra

      Public
      Agentic primative repository
      lyra
      Just
      •0•1•0•0•Updated Feb 20, 2026Feb 20, 2026

    • cellprofiler_processing

      Public
      CellProfiler data processing pipeline - feature selection, normalization, landmark analysis, and hierarchical clustering for Cell Painting high-throughput scree…
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • zarr-performance-testing

      Public
      Zarr performance testing
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • Segment-Flow

      Public
      Nextflow pipeline for deep learning segmentation models
      Python
      •2•6•0•1•Updated Feb 19, 2026Feb 19, 2026

    • aiod_utils

      Public
      Python
      •0•0•0•1•Updated Feb 19, 2026Feb 19, 2026

    • AIoD-Model-Registry

      Public
      The core registry for all AI models available on AI on Demand
      Python
      •1•3•2•0•Updated Feb 18, 2026Feb 18, 2026

    • introduction-to-image-analysis

      Public
      Jupyter Notebook
      •
      Creative Commons Attribution Share Alike 4.0 International
      •5•9•0•0•Updated Feb 13, 2026Feb 13, 2026

    • ai-on-demand

      Public
      Python
      •
      GNU General Public License v3.0
      •1•3•3•3•Updated Feb 13, 2026Feb 13, 2026

    • 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•4•4•0•Updated Feb 12, 2026Feb 12, 2026

    • JamiesonSwitch

      Public
      0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • pMANIC

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•11•0•Updated Feb 11, 2026Feb 11, 2026

    • Spatial-Biology-Pipeline

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • spc-cosine-analysis

      Public
      Cell Painting phenotypic analysis pipeline for SPC machine learning embeddings - distance metrics, landmark identification, compound scoring, and hierarchical c…
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 10, 2026Feb 10, 2026

    • nf-wgs-pf-dsl2

      Public
      Nextflow
      •2•0•0•0•Updated Feb 6, 2026Feb 6, 2026

    • napari_sam2

      Public
      Python
      •
      MIT License
      •0•1•17•3•Updated Jan 29, 2026Jan 29, 2026

    • sc-FOG-pub

      Public
      Public Repo for the Single Cell Python Analysis Workshop
      Jupyter Notebook
      •1•1•0•0•Updated Jan 28, 2026Jan 28, 2026

    • chipseq-w-spikein

      Public
      ChIP-seq peak-calling, QC and differential analysis pipeline with spikein
      Nextflow
      •
      MIT License
      •167•0•0•0•Updated Jan 19, 2026Jan 19, 2026

    • neuro-study-group

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Jan 19, 2026Jan 19, 2026

    • OmeSliCC

      Public
      Ome(ro) SLide Image Conversion and Compression pipline (OmeSliCC)
      ome-zarr-converter
      Python
      •
      Other
      •1•7•0•0•Updated Jan 16, 2026Jan 16, 2026

    • Enhancing-Reproducibility

      Public
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •0•4•0•0•Updated Jan 12, 2026Jan 12, 2026

    • from-notebook-to-pipeline

      Public
      work in progress for a new intermediate image analysis training workshop
      Jupyter Notebook
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•1•0•0•Updated Jan 6, 2026Jan 6, 2026

    • calm-mineo-miguel-aliaga

      Public
      Code for image analysis for "The sex and reproductive plasticity of intestinal muscles instruct gut size"
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 2, 2026Jan 2, 2026

    • RNU4-2_Saturation_Genome_Editing

      Public
      Code for analysis of RNU4-2 SGE
      Jupyter Notebook
      •0•2•0•0•Updated Dec 19, 2025Dec 19, 2025

    • CDC25-proj3-gerontogianni

      Public
      Single Cell Dim Reduction
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • CDC25-proj6-marzook

      Public
      Crispr Spatial Image Analysis
      Python
      •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • CrosstalkPy

      Public
      Python
      •0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • crypto-trail-analyser

      Public
      An image analysis pipeline to quantify Cryptosporidium trails
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • py-bioimage-qc

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 16, 2025Dec 16, 2025