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@PathologyDataScience

Computational and Integrative Pathology

Organization for the Computational and Integrative Pathology Group at Northwestern University

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  1. BCSS BCSS Public

    Use this to download all elements of the BCSS dataset described in: Amgad M, Elfandy H, ..., Gutman DA, Cooper LAD. Structured crowdsourcing enables convolutional segmentation of histology images. …

    Python 185 24

  2. SurvivalNet SurvivalNet Public

    Deep learning survival models

    Python 119 44

  3. SCNN SCNN Public

    Survival Convolutional Neural Networks

    67 21

  4. NuCLS NuCLS Public

    NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation

    Jupyter Notebook 57 14

  5. HiPS HiPS Public

    Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis

    Python 33 7

  6. MuTILs_Panoptic MuTILs_Panoptic Public

    Amgad M, Salgado R, Cooper LA. A panoptic segmentation approach for tumor-infiltrating lymphocyte assessment: development of the MuTILs model and PanopTILs dataset. medRxiv 2022.01.08.22268814.

    Python 30 7

Repositories

Showing 10 of 22 repositories
  • triteia Public

    A python client for pathology model inference with the Triton Inference Server.

    PathologyDataScience/triteia's past year of commit activity
    Jupyter Notebook 2 0 9 1 Updated Sep 18, 2026
  • MuTILs_Panoptic Public

    Amgad M, Salgado R, Cooper LA. A panoptic segmentation approach for tumor-infiltrating lymphocyte assessment: development of the MuTILs model and PanopTILs dataset. medRxiv 2022.01.08.22268814.

    PathologyDataScience/MuTILs_Panoptic's past year of commit activity
    Python 30 MIT 7 5 1 Updated Feb 6, 2026
  • ScanTools Public
    PathologyDataScience/ScanTools's past year of commit activity
    Python 2 Apache-2.0 1 1 0 Updated Jan 5, 2026
  • large_image_eager Public Forked from girder/large_image

    Integration of the eager iterator.

    PathologyDataScience/large_image_eager's past year of commit activity
    Python 1 Apache-2.0 51 0 0 Updated Mar 12, 2025
  • HiPS Public

    Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis

    PathologyDataScience/HiPS's past year of commit activity
    Python 33 MIT 7 1 0 Updated Apr 9, 2024
  • glimr Public

    A simplified wrapper for hyperparameter search with Ray Tune.

    PathologyDataScience/glimr's past year of commit activity
    Python 1 Apache-2.0 0 16 0 Updated Jan 22, 2024
  • HistomicsML2 Public

    A tool for training machine-learning models with whole-slide imaging datasets

    PathologyDataScience/HistomicsML2's past year of commit activity
    JavaScript 26 5 10 0 Updated Dec 27, 2023
  • HistomicsML Public

    An interactive machine learning framework for large histopathology images.

    PathologyDataScience/HistomicsML's past year of commit activity
    JavaScript 21 5 2 0 Updated Dec 27, 2023
  • SCNN Public

    Survival Convolutional Neural Networks

    PathologyDataScience/SCNN's past year of commit activity
    67 21 6 0 Updated Apr 2, 2023
  • SurvivalNet Public

    Deep learning survival models

    PathologyDataScience/SurvivalNet's past year of commit activity
    Python 119 Apache-2.0 44 10 3 Updated Dec 27, 2022
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