Repositories list

• NF1_organoid_cell_segmentation

  Public
  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

• waysciencelab.com

  Public
  Homepage for all happenings in the Way Lab at CU Anschutz

  data-sciencemachine-learningbiology+ 1health

  SCSS

  •

  BSD 3-Clause "New" or "Revised" License

  •9•4•2•0•Updated Aug 12, 2025Aug 12, 2025

• nViz

  Public
  A tool for creating and visualizing n-dimensional microscopy images.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •3•1•18•3•Updated Aug 12, 2025Aug 12, 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•5•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

• virtual_stain_flow

  Public
  For developing virtual staining models

  BSD 3-Clause "New" or "Revised" License

  •1•0•7•1•Updated Jul 25, 2025Jul 25, 2025

• gene_dependency_representations

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •5•3•2•1•Updated Jul 23, 2025Jul 23, 2025

• JUMP-single-cell

  Public
  Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)

  pythonimage-processingcellprofiler+ 3image-analysiscell-paintingpycytominer

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •5•4•2•1•Updated Jul 23, 2025Jul 23, 2025

• buscar

  Public
  Jupyter Notebook

  •1•1•4•3•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

• cellpainting_predicts_cardiac_fibrosis

  Public
  Image-based profiling and machine learning to predict failing vs. non-failing cardiac fibroblasts

  machine-learningimage-processingcellprofiler+ 3cell-paintingimage-based-analysispycytominer

  Jupyter Notebook

  •

  Other

  •1•5•3•0•Updated Jul 15, 2025Jul 15, 2025

• playbooks

  Public
  Playbooks relevant to the operations of the Way Lab and similar labs.

  Shell

  •

  Creative Commons Zero v1.0 Universal

  •1•0•5•1•Updated Jul 14, 2025Jul 14, 2025

• NF1_3D_organoid_profiling_pipeline

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •2•3•21•12•Updated Jul 3, 2025Jul 3, 2025

• NF1_2D_organoid_profiling_pipeline

  Public
  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •2•0•0•3•Updated Jul 2, 2025Jul 2, 2025

• live_cell_timelapse_apoptosis_analysis

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•2•0•Updated Jun 27, 2025Jun 27, 2025

• live_cell_timelapse_apoptosis

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •3•1•6•0•Updated Jun 26, 2025Jun 26, 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

  •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

• 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

• 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