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@WayScience

The Way Lab

The Way Lab at CU Anschutz
README.md

Welcome to the open-source GitHub organization hosted by The Way Lab.

We are a team of scientists and engineers developing methods and software for analyzing microscopy images of cells. Our mission is to reduce human suffering.

Our website contains complete details of our research projects, team members, and funding: https://www.waysciencelab.com/

Check out a few of our open-source projects!

Publications

Tomkinson, J., Kern, R., Mattson, C. et al. Toward generalizable phenotype prediction from single-cell morphology representations. BMC Methods 1, 17 (2024). doi: https://doi.org/10.1186/s44330-024-00014-3; GitHub Repository: https://github.com/WayScience/phenotypic_profiling/

Lippincott, M.J., Tomkinson, J., Bunten, D. et al. A morphology and secretome map of pyroptosis. bioRxiv 2024.04.26.591386; doi: https://doi.org/10.1101/2024.04.26.591386; GitHub Repository: https://github.com/WayScience/pyroptosis_signature_data_analysis

Serrano, E., Chandrasekaran, S.N., Bunten, D. et al. Reproducible image-based profiling with Pycytominer. Nat Methods (2025). doi: https://doi.org/10.1038/s41592-025-02611-8; GitHub Repository: https://github.com/cytomining/pycytominer

Software

Projects

We are leading multidisciplinary scientists in a variety of team-science initiatives.

Pediatric Cancer Cell Morphology Atlas

We are developing a reference Cell Painting data set of pediatric cancer cell lines, and performing several high-throughput, high-content phenotypic drug screens.

3D profiling of Neurofibromatosis Type 1 patient-derived organoids

We are developing a 3D image analysis pipeline to profile patient-derived organoids from neurofibromatosis type 1 (NF1) patients, and we will be performing several high-throughput, high-content phenotypic drug screens.

Finding new therapeutics for cardiac fibrosis

We are identifying fundamental differences between cardiac fibroblasts from patients with and without heart failure, and we are developing a high-throughput, high-content phenotypic drug screen to identify new therapeutics for cardiac fibrosis.

Pinned Loading

  1. phenotypic_profiling phenotypic_profiling Public

    Machine learning for predicting 15 single-cell phenotypes from cell morphology profiles

    Jupyter Notebook 2 3

  2. nf1_schwann_cell_painting_data 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 5 5

  3. pyroptosis_signature_image_profiling pyroptosis_signature_image_profiling Public

    This repository contains the pipelines used to analyze the data sets from the Interstellar collaboration.

    Jupyter Notebook 3 3

  4. coSMicQC coSMicQC Public

    Single cell Morphology Quality Control (coSMicQC)

    Python 7 3

  5. predicting-cell-injury-compounds 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 1 2

  6. CPBS7601 CPBS7601 Public

    Course on computing skills in biomedical informatics

    Jupyter Notebook 9

Repositories

Showing 10 of 80 repositories
  • 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.

    WayScience/nf1_schwann_cell_morphology_signature’s past year of commit activity
    Jupyter Notebook 0 CC0-1.0 2 1 1 Updated Apr 1, 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.

    WayScience/nf1_schwann_cell_painting_data’s past year of commit activity
    Jupyter Notebook 5 CC0-1.0 5 6 0 Updated Apr 1, 2025
  • live_cell_timelapse_apoptosis_analysis Public
    WayScience/live_cell_timelapse_apoptosis_analysis’s past year of commit activity
    0 BSD-3-Clause 1 1 0 Updated Apr 1, 2025
  • CFReT-screen-mAP-analysis Public

    Analysis notebooks applying mean average Precision (mAP) to the CFReT screen image-based profiles dataset.

    WayScience/CFReT-screen-mAP-analysis’s past year of commit activity
    Jupyter Notebook 0 1 3 0 Updated Apr 1, 2025
  • NF1_3D_organoid_profiling_pipeline Public
    WayScience/NF1_3D_organoid_profiling_pipeline’s past year of commit activity
    Jupyter Notebook 2 BSD-3-Clause 2 7 3 Updated Apr 1, 2025
  • live_cell_timelapse_apoptosis Public
    WayScience/live_cell_timelapse_apoptosis’s past year of commit activity
    Jupyter Notebook 1 BSD-3-Clause 2 5 2 Updated Apr 1, 2025
  • coSMicQC Public

    Single cell Morphology Quality Control (coSMicQC)

    WayScience/coSMicQC’s past year of commit activity
    Python 7 BSD-3-Clause 3 20 1 Updated Mar 31, 2025
  • collaborator_map Public
    WayScience/collaborator_map’s past year of commit activity
    HTML 0 BSD-3-Clause 1 0 0 Updated Mar 31, 2025
  • CytoDataFrame Public

    An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.

    WayScience/CytoDataFrame’s past year of commit activity
    Python 1 BSD-3-Clause 2 13 0 Updated Mar 31, 2025
  • .github Public
    WayScience/.github’s past year of commit activity
    0 BSD-3-Clause 0 0 0 Updated Mar 31, 2025
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