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@PathologyDataScience Computational and Integrative Pathology

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    19 repositories

    • HiPS

      Public
      Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
      biomedical-image-processingbiomarker-discoverydigital-pathologybreast-cancercomputational-pathologyexplainable-aisurvival-prediction
      Python
      •
      MIT License
      •4•19•0•0•Updated Apr 9, 2024Apr 9, 2024

    • glimr

      Public
      A simplified wrapper for hyperparameter search with Ray Tune.
      Python
      •
      Apache License 2.0
      •0•1•9•0•Updated Jan 22, 2024Jan 22, 2024

    • HistomicsML2

      Public
      A tool for training machine-learning models with whole-slide imaging datasets
      JavaScript
      •5•22•10•0•Updated Dec 27, 2023Dec 27, 2023

    • HistomicsML

      Public
      An interactive machine learning framework for large histopathology images.
      JavaScript
      •5•19•2•0•Updated Dec 27, 2023Dec 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.
      deep-learningconvolutional-neural-networksdigital-pathologybreast-cancercomputational-pathologyexplainable-aitumor-segmentationtumor-infiltrating-lymphocytes
      Python
      •
      MIT License
      •3•12•3•0•Updated May 19, 2023May 19, 2023

    • SCNN

      Public
      Survival Convolutional Neural Networks
      19•68•6•0•Updated Apr 2, 2023Apr 2, 2023

    • SurvivalNet

      Public
      Deep learning survival models
      Python
      •
      Apache License 2.0
      •44•116•10•3•Updated Dec 27, 2022Dec 27, 2022

    • MiscSurvivalUtils

      Public
      Miscellaneous tools for data management and classical survival analysis.
      Python
      •0•3•0•0•Updated Dec 10, 2022Dec 10, 2022

    • NuCLS

      Public
      NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation
      Jupyter Notebook
      •
      MIT License
      •13•46•3•0•Updated Apr 4, 2022Apr 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
      Python
      •
      MIT License
      •16•140•4•0•Updated Apr 1, 2022Apr 1, 2022

    • histolab

      Public
      Library for Digital Pathology Image Processing
      Python
      •
      Apache License 2.0
      •59•6•0•0•Updated Aug 23, 2021Aug 23, 2021

    • RipleyK

      Public
      Calculation of the Ripley K (spatial statistics) value in python
      Python
      •
      MIT License
      •3•0•0•0•Updated May 17, 2021May 17, 2021

    • hif2gene

      Public
      Jupyter Notebook
      •
      Other
      •14•2•0•0•Updated Feb 10, 2021Feb 10, 2021

    • pathology-hooknet

      Public
      Python
      •10•0•0•0•Updated Jan 15, 2021Jan 15, 2021

    • HistomicsTK

      Public
      A Python library for pathology image analysis algorithms.
      Python
      •
      Apache License 2.0
      •117•4•0•0•Updated Sep 15, 2020Sep 15, 2020

    • IHC-Analysis

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Feb 25, 2019Feb 25, 2019

    • Mask_RCNN

      Public
      Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow
      Python
      •
      Other
      •12k•1•0•0•Updated Jul 12, 2018Jul 12, 2018

    • MatDigitalPathology

      Public
      Matlab functions to support analysis of digital pathology images.
      cancermatlabimage-processingimage-analysismicroscopyimage-analysis-workflowsdigital-pathology
      MATLAB
      •3•5•0•0•Updated Feb 21, 2017Feb 21, 2017

    • HistXtract

      Public
      A pipeline for extracting nuclear morphometry features from whole-slide images.
      MATLAB
      •
      Apache License 2.0
      •3•3•0•0•Updated Feb 21, 2017Feb 21, 2017