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    102 repositories

    • 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 Jul 28, 2026Jul 28, 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 Jul 28, 2026Jul 28, 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 Jul 27, 2026Jul 27, 2026

    • NF1_3D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•4•12•4•Updated Jul 27, 2026Jul 27, 2026

    • nuclear_speckles_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•2•0•Updated Jul 27, 2026Jul 27, 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 Jul 26, 2026Jul 26, 2026

    • virtual_stain_flow

      Public
      For developing virtual staining models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•7•1•Updated Jul 25, 2026Jul 25, 2026

    • buscar

      Public
      Single cell hit calling for high-content screens
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•7•6•8•Updated Jul 24, 2026Jul 24, 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•2•Updated Jul 20, 2026Jul 20, 2026

    • ZedProfiler

      Public
      Featurizing high-content 3D microscopy image
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•2•5•5•Updated Jul 20, 2026Jul 20, 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 Jul 17, 2026Jul 17, 2026

    • pyroptosis_live-cell_timelapse

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

    • live_cell_timelapse_apoptosis_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•0•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

    • ome-arrow-benchmarks

      Public
      Benchmarking OME Arrow through Parquet, Vortex, LanceDB, and more.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•5•2•Updated Jul 15, 2026Jul 15, 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

    • 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 Jul 1, 2026Jul 1, 2026

    • gene-process-dependencies

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•4•2•2•Updated Jul 1, 2026Jul 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 Jul 1, 2026Jul 1, 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•1•Updated Jun 24, 2026Jun 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•0•Updated Jun 22, 2026Jun 22, 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

    • pccma_repo1_screen_image_profiling

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•0•Updated Jun 11, 2026Jun 11, 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•4•3•0•Updated May 29, 2026May 29, 2026

    • pediatric_cancer_atlas_analysis

      Public
      Image2Image Translation Model Optimization and Training to Predict Stains from Brightfield with Cell Painting Data
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•2•Updated May 25, 2026May 25, 2026

    • US_TIE_Zhang_et_al_2020_py

      Public
      Python package for transport-of-intensity equation ported from MATLAB to Python using Claude Sonnet 4.6
      Python
      •
      Other
      •1•1•0•0•Updated May 23, 2026May 23, 2026

    • NF1_2D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •2•0•2•1•Updated Apr 8, 2026Apr 8, 2026
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