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    91 repositories

    • 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•2•1•5•Updated Feb 3, 2026Feb 3, 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
      •3•3•11•0•Updated Feb 2, 2026Feb 2, 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•2•Updated Feb 1, 2026Feb 1, 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 Jan 30, 2026Jan 30, 2026

    • NF1_3D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•4•31•2•Updated Jan 30, 2026Jan 30, 2026

    • buscar

      Public
      Jupyter Notebook
      •1•2•10•1•Updated Jan 25, 2026Jan 25, 2026

    • JUMP-single-cell

      Public
      Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)
      pythonimage-processingcellprofilerimage-analysiscell-paintingpycytominer
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•4•2•2•Updated Jan 23, 2026Jan 23, 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•1•Updated Jan 23, 2026Jan 23, 2026

    • NF1_organoid_cell_segmentation

      Public
      Deep learning–based vision model for segmentation of cells within NF1 organoids.
      data-sciencemachine-learningdeep-learningartificial-intelligencedata-wranglingcell-biology
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Jan 16, 2026Jan 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•2•5•Updated Jan 13, 2026Jan 13, 2026

    • virtual_stain_flow

      Public
      For developing virtual staining models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•3•0•Updated Jan 12, 2026Jan 12, 2026

    • CPBS7601

      Public
      Course on computing skills in biomedical informatics
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •21•5•0•1•Updated Jan 8, 2026Jan 8, 2026

    • predicting_cardiac_fibrosis_etiologies

      Public
      Jupyter Notebook
      •
      Other
      •1•0•4•1•Updated Jan 6, 2026Jan 6, 2026

    • NF1_2D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •2•0•2•1•Updated Dec 29, 2025Dec 29, 2025

    • nViz

      Public
      A tool for creating and visualizing n-dimensional microscopy images.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•26•5•Updated Dec 22, 2025Dec 22, 2025

    • PRISM_Agent_LITL_experiments

      Public
      Exploring how to better utilize Lab In The Loop (LITL) data in agentic systems with DSPy. Built with DSPy, this repo provides modular agent tools and academic …
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•1•Updated Dec 12, 2025Dec 12, 2025

    • MIICE

      Public
      MIICE performs evaluation on microscopy images for issues with image quality (illumination and contrast).
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•5•0•Updated Dec 10, 2025Dec 10, 2025

    • serpula_rasa

      Public
      Blank snake implementation prototype for image-based single-cell profiling
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•1•Updated Nov 24, 2025Nov 24, 2025

    • 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 Nov 19, 2025Nov 19, 2025

    • gene-process-dependencies

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•4•2•0•Updated Nov 14, 2025Nov 14, 2025

    • AmemDSPy

      Public
      A refactored agentic memory for LLM agents using the DSPy LM interface, integrating metadata based precise match search on top of existing embedding-similarity …
      Python
      •
      MIT License
      •90•0•0•1•Updated Nov 3, 2025Nov 3, 2025

    • waysciencelab.com

      Public
      Homepage for all happenings in the Way Lab at CU Anschutz
      data-sciencemachine-learningbiologyhealth
      SCSS
      •
      BSD 3-Clause "New" or "Revised" License
      •11•4•2•0•Updated Oct 31, 2025Oct 31, 2025

    • live_cell_timelapse_apoptosis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•6•0•Updated Oct 22, 2025Oct 22, 2025

    • live_cell_timelapse_apoptosis_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•0•Updated Oct 22, 2025Oct 22, 2025

    • demo-vs-code-notebook-root

      Public
      Demonstrating how to set a notebook root for vs code through a repository.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•1•Updated Sep 23, 2025Sep 23, 2025

    • 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 Sep 18, 2025Sep 18, 2025

    • cellpainting_predicts_cardiac_fibrosis

      Public
      Image-based profiling and machine learning to predict failing vs. non-failing cardiac fibroblasts
      machine-learningimage-processingcellprofilercell-paintingimage-based-analysispycytominer
      Jupyter Notebook
      •
      Other
      •1•5•3•0•Updated Sep 15, 2025Sep 15, 2025

    • breast_cancer_cell_painting_profiling

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 10, 2025Sep 10, 2025

    • sandbox

      Public
      A place to mess around learning github
      MIT License
      •24•0•0•3•Updated Sep 2, 2025Sep 2, 2025

    • Phenotypic_severity_and_variance

      Public
      Quantifying Zebrafish opercle bone morphology
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•1•0•Updated Aug 5, 2025Aug 5, 2025