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    90 repositories

    • virtual_stain_flow

      Public
      For developing virtual staining models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•4•1•Updated Dec 9, 2025Dec 9, 2025

    • NF1_3D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•27•3•Updated Dec 7, 2025Dec 7, 2025

    • 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•0•0•Updated Dec 5, 2025Dec 5, 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 experiments on PRISM-inspired drug repurposing data to test agentic system improvement under different toolsets.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•2•Updated Dec 4, 2025Dec 4, 2025

    • 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•0•Updated Dec 3, 2025Dec 3, 2025

    • predicting_cardiac_fibrosis_etiologies

      Public
      Jupyter Notebook
      •
      Other
      •1•0•2•1•Updated Dec 2, 2025Dec 2, 2025

    • napari-ome-arrow

      Public
      A Napari plugin for OME-Arrow and OME-Parquet bioimage data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Dec 1, 2025Dec 1, 2025

    • nViz

      Public
      A tool for creating and visualizing n-dimensional microscopy images.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•26•4•Updated Nov 29, 2025Nov 29, 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

    • 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•1•Updated Nov 21, 2025Nov 21, 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•4•3•1•Updated Nov 19, 2025Nov 19, 2025

    • 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 Nov 18, 2025Nov 18, 2025

    • gene-process-dependencies

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

    • 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•1•Updated Nov 14, 2025Nov 14, 2025

    • buscar

      Public
      Jupyter Notebook
      •1•1•8•1•Updated Nov 11, 2025Nov 11, 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 search.
      Python
      •
      MIT License
      •84•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

    • CPBS7601

      Public
      Course on computing skills in biomedical informatics
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •20•5•0•1•Updated Oct 21, 2025Oct 21, 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
      •1•0•0•0•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

    • NF1_2D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •2•0•2•2•Updated Sep 13, 2025Sep 13, 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

    • nf1_schwann_cell_painting_data

      Public
      This repository contains all the modules to perform image-based analysis with CellProfiler on NF1 Schwann cell data.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •6•6•5•0•Updated Jul 28, 2025Jul 28, 2025

    • nf1_schwann_cell_morphology_signature

      Public
      This repository contains all the modules to split and train a binary classification model to predict NF1 null and wildtype genotype.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • 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•7•0•Updated Jun 26, 2025Jun 26, 2025