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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 140 16

  2. SurvivalNet SurvivalNet Public

    Deep learning survival models

    Python 116 44

  3. SCNN SCNN Public

    Survival Convolutional Neural Networks

    68 19

  4. NuCLS NuCLS Public

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

    Jupyter Notebook 46 13

  5. HistomicsML2 HistomicsML2 Public

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

    JavaScript 22 5

  6. HistomicsML HistomicsML Public

    An interactive machine learning framework for large histopathology images.

    JavaScript 19 5

Repositories

Showing 10 of 19 repositories
  • 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 18 MIT 3 0 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 9 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 22 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 19 5 2 0 Updated Dec 27, 2023
  • 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 12 MIT 2 3 0 Updated May 19, 2023
  • SCNN Public

    Survival Convolutional Neural Networks

    PathologyDataScience/SCNN’s past year of commit activity
    68 19 6 0 Updated Apr 2, 2023
  • SurvivalNet Public

    Deep learning survival models

    PathologyDataScience/SurvivalNet’s past year of commit activity
    Python 116 Apache-2.0 44 10 3 Updated Dec 27, 2022
  • MiscSurvivalUtils Public

    Miscellaneous tools for data management and classical survival analysis.

    PathologyDataScience/MiscSurvivalUtils’s past year of commit activity
    Python 3 0 0 0 Updated Dec 10, 2022
  • NuCLS Public

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

    PathologyDataScience/NuCLS’s past year of commit activity
    Jupyter Notebook 46 MIT 13 3 0 Updated Apr 4, 2022
  • 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. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz083

    PathologyDataScience/BCSS’s past year of commit activity
    Python 140 MIT 16 4 0 Updated Apr 1, 2022
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