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    104 repositories

    • gene-process-dependencies

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•4•2•1•Updated Aug 26, 2026Aug 26, 2026

    • NF1_3D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •4•4•13•1•Updated Aug 26, 2026Aug 26, 2026

    • NF1_organoid_profile_analysis

      Public
      This repo contains analysis code of profiles generated in multiple image-based profiling repos.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•1•9•Updated Aug 25, 2026Aug 25, 2026

    • pccma_repo1_screen_image_profiling

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•0•Updated Aug 24, 2026Aug 24, 2026

    • targeted_fibrosis_drug_screen

      Public
      Image analysis and image-based profiling of a fibrosis drug screen to identify compound hits using a machine learning model.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •5•3•12•2•Updated Aug 24, 2026Aug 24, 2026

    • tesserift

      Public
      Measure how bioimaging storage layouts shape performance, analysis, and biological discovery.
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Aug 19, 2026Aug 19, 2026

    • aberrant_nuclear_speckle_phenotype_treatment_analysis

      Public
      For detecting treatments causing aberrant nuclear speckle phenotypes.
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Aug 19, 2026Aug 19, 2026

    • habomero

      Public
      Reproducible server-style OMERO deployment for Linux workstations using Docker Compose, Ansible, and uv.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Aug 18, 2026Aug 18, 2026

    • nuclear_speckles_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•2•0•Updated Aug 18, 2026Aug 18, 2026

    • NF1_organoid_cell_segmentation

      Public
      Deep learning–based vision model for segmentation of cells within NF1 organoids.
      data-sciencemachine-learningdeep-learning
      data-sciencemachine-learningdeep-learningartificial-intelligencedata-wranglingcell-biology
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•1•Updated Aug 17, 2026Aug 17, 2026

    • jump_image_data_downloader

      Public
      Allows JUMP users to download JUMP images by filtering JUMP image metadata.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•1•Updated Aug 12, 2026Aug 12, 2026

    • ZedProfiler

      Public
      Featurizing high-content 3D microscopy images
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•6•3•Updated Aug 12, 2026Aug 12, 2026

    • live_cell_timelapse_apoptosis_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•1•Updated Aug 11, 2026Aug 11, 2026

    • playbooks

      Public
      Playbooks relevant to the operations of the Way Lab and similar labs.
      Shell
      •
      Creative Commons Zero v1.0 Universal
      •3•0•8•0•Updated Aug 10, 2026Aug 10, 2026

    • OME-IRIS

      Public
      Open Microscopy Environment (OME) Interoperable Reference Imaging Sets (IRIS) for reproducible benchmarking and validation of imaging data, analytical outputs, …
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Aug 10, 2026Aug 10, 2026

    • iceberg-bioimage

      Public
      A format-agnostic framework for cataloging and querying bioimaging data (Parquet, OME-Zarr, OME-TIFF) with Apache Iceberg
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•2•0•Updated Aug 10, 2026Aug 10, 2026

    • buscar

      Public
      Single cell hit calling for high-content screens
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•7•6•8•Updated Aug 7, 2026Aug 7, 2026

    • virtual_stain_flow

      Public
      For developing virtual staining models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•7•2•Updated Aug 6, 2026Aug 6, 2026

    • pediatric_cancer_atlas_profiling

      Public
      Image analysis and image-based profiling of pediatic cancer cell lines to extract morphological profiles.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •5•7•3•0•Updated Aug 5, 2026Aug 5, 2026

    • ome-arrow

      Public
      Using OME specifications with Apache Arrow for fast, queryable, and language agnostic bioimage data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•7•0•Updated Aug 4, 2026Aug 4, 2026

    • ome-arrow-benchmarks

      Public
      Benchmarking OME Arrow through Parquet, Vortex, LanceDB, and more.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•5•3•Updated Aug 1, 2026Aug 1, 2026

    • napari-ome-arrow

      Public
      A Napari plugin for OME-Arrow and OME-Parquet bioimage data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•1•3•Updated Aug 1, 2026Aug 1, 2026

    • pyroptosis_live-cell_timelapse

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•3•Updated Jul 16, 2026Jul 16, 2026

    • live_cell_timelapse_apoptosis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•6•1•Updated Jul 16, 2026Jul 16, 2026

    • duckdb_zarr

      Public archive
      A DuckDB extension for querying Zarr arrays with SQL through relational projection.
      C++
      •
      MIT License
      •1•7•0•0•Updated Jul 11, 2026Jul 11, 2026

    • waysciencelab.com

      Public
      Homepage for all happenings in the Way Lab at CU Anschutz
      data-sciencemachine-learningbiology
      data-sciencemachine-learningbiologyhealth
      SCSS
      •
      BSD 3-Clause "New" or "Revised" License
      •11•4•2•0•Updated Jul 10, 2026Jul 10, 2026

    • Buscar-benchmark-analysis

      Public
      Contains analysis that was used to benchmark Buscar
      Jupyter Notebook
      •1•0•7•0•Updated Jun 15, 2026Jun 15, 2026

    • .github

      Public
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jun 10, 2026Jun 10, 2026

    • predicting_cardiac_fibrosis_etiologies

      Public
      Predicting cardiac fibrosis etiologies through machine learning using morphology profiles acquired from Cell Painting cardiac fibroblasts.
      Jupyter Notebook
      •
      Other
      •2•0•4•0•Updated Jun 1, 2026Jun 1, 2026

    • JUMP-single-cell

      Public
      Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)
      pythonimage-processingcellprofiler
      pythonimage-processingcellprofilerimage-analysiscell-paintingpycytominer
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•5•3•0•Updated May 29, 2026May 29, 2026
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