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    100 repositories

    • nuclear_speckles_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•1•Updated May 27, 2026May 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•6•0•Updated May 27, 2026May 27, 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

    • 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•1•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
      •0•0•0•0•Updated May 23, 2026May 23, 2026

    • buscar

      Public
      Single cell hit calling for high-content screens
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•6•6•4•Updated May 22, 2026May 22, 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•1•Updated May 21, 2026May 21, 2026

    • ZedProfiler

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•3•1•Updated May 16, 2026May 16, 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 May 14, 2026May 14, 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
      •1•1•1•1•Updated May 9, 2026May 9, 2026

    • playbooks

      Public
      Playbooks relevant to the operations of the Way Lab and similar labs.
      Shell
      •
      Creative Commons Zero v1.0 Universal
      •2•0•8•0•Updated May 8, 2026May 8, 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•0•Updated May 7, 2026May 7, 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•0•Updated May 4, 2026May 4, 2026

    • Buscar-benchmark-analysis

      Public
      Contains analysis that was used to benchmark Buscar
      Jupyter Notebook
      •1•0•3•0•Updated May 1, 2026May 1, 2026

    • virtual_stain_flow

      Public
      For developing virtual staining models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•5•1•Updated Apr 30, 2026Apr 30, 2026

    • pccma_repo1_screen_image_profiling

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Apr 28, 2026Apr 28, 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 Apr 27, 2026Apr 27, 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
      •4•3•12•1•Updated Apr 10, 2026Apr 10, 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

    • meerqat

      Public
      Validate bioimaging datasets by detecting missing files, metadata gaps, and structural inconsistencies early.
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Mar 30, 2026Mar 30, 2026

    • nuclear_speckle_image_profiling

      Public
      Image analyis and image-based profiling of nuclear speckle dataset extracting intensity based features.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • duckdb_zarr

      Public
      A DuckDB extension for querying Zarr arrays with SQL through relational projection.
      C++
      •
      MIT License
      •1•6•0•0•Updated Mar 29, 2026Mar 29, 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•0•Updated Mar 27, 2026Mar 27, 2026

    • NF1_3D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•4•11•1•Updated Mar 24, 2026Mar 24, 2026

    • nViz

      Public
      A tool for creating and visualizing n-dimensional microscopy images.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•26•6•Updated Mar 16, 2026Mar 16, 2026

    • pccma_atlas_image_profiling

      Public
      Image analysis and image-based profiling workflows to extract morphology profiles from the PCCMA Atlas dataset.
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Mar 10, 2026Mar 10, 2026

    • demo-cellprofiler

      Public
      Demonstrating various CellProfiler development or implementations.
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Mar 8, 2026Mar 8, 2026

    • pyroptosis_live-cell_timelapse

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•3•Updated Mar 6, 2026Mar 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•6•3•1•Updated Feb 10, 2026Feb 10, 2026

    • CPBS7601

      Public
      Course on computing skills in biomedical informatics
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •21•5•0•2•Updated Jan 8, 2026Jan 8, 2026
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