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    85 repositories

    • CPBS7601

      Public
      Course on computing skills in biomedical informatics
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •9•2•0•0•Updated Sep 15, 2025Sep 15, 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_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•1•Updated Sep 13, 2025Sep 13, 2025

    • NF1_3D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•26•0•Updated Sep 13, 2025Sep 13, 2025

    • NF1_2D_organoid_profiling_pipeline

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

    • nViz

      Public
      A tool for creating and visualizing n-dimensional microscopy images.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•21•2•Updated Sep 13, 2025Sep 13, 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
      •0•1•0•1•Updated Sep 12, 2025Sep 12, 2025

    • buscar

      Public
      Jupyter Notebook
      •1•1•13•2•Updated Sep 12, 2025Sep 12, 2025

    • live_cell_timelapse_apoptosis_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•3•Updated Sep 11, 2025Sep 11, 2025

    • breast_cancer_cell_painting_profiling

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

    • live_cell_timelapse_apoptosis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•6•1•Updated Sep 10, 2025Sep 10, 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.
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Sep 10, 2025Sep 10, 2025

    • virtual_stain_flow

      Public
      For developing virtual staining models
      BSD 3-Clause "New" or "Revised" License
      •1•0•7•1•Updated Sep 9, 2025Sep 9, 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 Sep 8, 2025Sep 8, 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 Sep 4, 2025Sep 4, 2025

    • sandbox

      Public
      A place to mess around learning github
      MIT License
      •23•0•0•2•Updated Sep 2, 2025Sep 2, 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
      •10•4•2•0•Updated Aug 28, 2025Aug 28, 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

    • 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•2•1•Updated Jul 29, 2025Jul 29, 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
      •5•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
      •2•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • gene_dependency_representations

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•4•2•1•Updated Jul 23, 2025Jul 23, 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 Jul 18, 2025Jul 18, 2025

    • playbooks

      Public
      Playbooks relevant to the operations of the Way Lab and similar labs.
      Shell
      •
      Creative Commons Zero v1.0 Universal
      •1•0•6•1•Updated Jul 14, 2025Jul 14, 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
      •2•3•7•0•Updated Jun 26, 2025Jun 26, 2025

    • demo-uca-isilon-python

      Public
      Demonstrating capabilities with the University of Colorado Anschutz (UCA) Isilon storage solution using Python.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•5•0•Updated Jun 24, 2025Jun 24, 2025

    • nuclear_speckles_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•0•Updated Jun 19, 2025Jun 19, 2025

    • ForestWizard

      Public
      A wizard to guide you through the forest of single-cell data.
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Jun 6, 2025Jun 6, 2025

    • .github

      Public
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated May 23, 2025May 23, 2025

    • MNIST_TD-VAE

      Public
      Temporal Difference Variational Auto-Encoder (TD-VAE) (Implementation in PyTorch)
      Python
      •31•0•0•0•Updated May 14, 2025May 14, 2025