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    80 repositories

    • 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 10, 2025Jun 10, 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

    • NF1_3D_organoid_profiling_pipeline

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

    • live_cell_timelapse_apoptosis_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•1•Updated Jun 5, 2025Jun 5, 2025

    • playbooks

      Public
      Playbooks relevant to the operations of the Way Lab and similar labs.
      Creative Commons Zero v1.0 Universal
      •1•0•5•1•Updated Jun 3, 2025Jun 3, 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•1•2•Updated May 29, 2025May 29, 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 May 29, 2025May 29, 2025

    • nuclear_speckles_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•0•Updated May 23, 2025May 23, 2025

    • .github

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

    • live_cell_timelapse_apoptosis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•6•1•Updated May 22, 2025May 22, 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•1•Updated May 21, 2025May 21, 2025

    • nViz

      Public
      A tool for creating and visualizing n-dimensional microscopy images.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•16•5•Updated May 20, 2025May 20, 2025

    • MNIST_TD-VAE

      Public
      Temporal Difference Variational Auto-Encoder (TD-VAE) (Implementation in PyTorch)
      Python
      •30•0•0•0•Updated May 14, 2025May 14, 2025

    • pairwise_compare

      Public
      Allows the user to compare groups of data specified in a tidy pandas dataframe with ease.
      groupsanalysispandas-dataframe
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•3•0•Updated May 7, 2025May 7, 2025

    • CFReT-screen-mAP-analysis

      Public
      Analysis notebooks applying mean average Precision (mAP) to the CFReT screen image-based profiles dataset.
      Jupyter Notebook
      •1•0•5•0•Updated May 1, 2025May 1, 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 Apr 24, 2025Apr 24, 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 Apr 23, 2025Apr 23, 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•5•5•0•Updated Apr 23, 2025Apr 23, 2025

    • gene_dependency_representations

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

    • collaborator_map

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Mar 31, 2025Mar 31, 2025

    • pyroptosis_signature_data_analysis

      Public
      Analysis repository for the pyroptosis morphology map
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•15•0•Updated Mar 25, 2025Mar 25, 2025

    • pyroptosis_live-cell_timelapse

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Mar 17, 2025Mar 17, 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
      •9•4•2•0•Updated Mar 11, 2025Mar 11, 2025

    • pediatric_cancer_atlas_analysis

      Public
      Image2Image Translation Model Optimization and Training to Predict Stains from Brightfield with Cell Painting Data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Mar 6, 2025Mar 6, 2025

    • sc-tracking-optimization

      Public
      This repo aims to track cells in the best way possible
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Feb 25, 2025Feb 25, 2025

    • virtual_stain_flow

      Public
      For developing virtual staining models
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Feb 14, 2025Feb 14, 2025

    • gc-saguaro_udm_bucket

      Public
      Cloud Storage bucket on Google Cloud for Saguaro and UdeM data transfer.
      cloudresourcebucket
      CUE
      •1•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • CPBS7601

      Public
      Course on computing skills in biomedical informatics
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •9•2•0•1•Updated Jan 14, 2025Jan 14, 2025

    • gc-bucket-alsf-predicting-nuclear-speckles

      Public archive
      GCP bucket for ALSF collaborations on predicting nuclear speckles. (now archived outside of these cloud resources)
      cloud-resourcesbucket
      HCL
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Jan 14, 2025Jan 14, 2025

    • predicting-cell-injury-compounds

      Public
      Processing cell-injury profiles using Pycytominer to generate selected features profiles for training a multi-class regression model to identify cellular injury.
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •2•1•0•0•Updated Dec 24, 2024Dec 24, 2024