computational-pathology

There are 80 repositories under computational-pathology topic.

  • PCAM-Pipeline

    Language:Python1

  • torchvahadane

    Gpu accelerated vahadane stain normalization for Digital Pathology workflows.

    Language:Python14

  • good-features

    Official code for the paper "A Good Feature Extractor Is All You Need for Weakly Supervised Pathology Slide Classification"

    Language:Jupyter Notebook13

  • simple_wsi_viewer

    A simple web application for for viewing and navigating pathology whole-slide-images in your browser.

    Language:JavaScript12

  • CPATH_demographics

    Demographic bias in misdiagnosis by computational pathology models - Nature Medicine

    Language:Python12

  • ConSlide

    [ICCV 2023] ConSlide: Asynchronous Hierarchical Interaction Transformer with Breakup-Reorganize Rehearsal for Continual Whole Slide Image Analysis

    Language:Python10

  • LNMNet

    Official Pytorch Implementation of our new paper 'Predicting Lymph Node Metastasis from Primary Cervical Cancer Based on Deep Learning in Histopathological Images.'

    Language:Python10
  • ThyroidRule

    ThyroidRule

    Rule-Based Thyroid Whole Slide Image Diagnosis

    Language:Python10

  • ThyroidInteractive

    Suspicious Regions-Based Whole Slide Image Analysis

    Language:Python10

  • GraphLSurv

    GraphLSurv: A Scalable Survival Prediction Network with Adaptive and Sparse Structure Learning for Histopathological Whole-Slide Images

    Language:Jupyter Notebook9

  • MuTILs_Panoptic

    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.

    Language:Python8

  • MulGT

    [AAAI'23] MulGT: Multi-task Graph-Transformer with Task-aware Knowledge Injection and Domain Knowledge-driven Pooling for Whole Slide Image Analysis

    Language:Python7

  • NucleiSegHE

    H&E ROI-Level and WSI-Level Nuclei Segmentation with HoVer-Net

    Language:Python6

  • collagen-fiber-metrics

    Deep generative models for collagen fiber centerline segmentation and extraction in cancer tissue

    Language:Jupyter Notebook6

  • annotated-papers

    Contains all research papers read since the end of July 2020 :+1:

    Language:Python6

  • Computational-Pathology-Reading-List

    Reading list for Computational Pathology

    6

  • Cox_AMIL

    Code for our BVM workshop submission "Attention-based Multiple Instance Learning for Survival Prediction on Lung Cancer Tissue Microarrays"

    Language:Jupyter Notebook5

  • gnn-pccp

    Graph neural networks for PDAC vs CP in histology

    Language:Jupyter Notebook5

  • DARTS-ADP

    Probeable DARTS with Application to Computational Pathology [ICCV2021]

    Language:Python5

  • Pyramidal-TIFF

    Convert Slides/Images to Pyramidal TIFF Format

    Language:Python4

  • elm-asap-pathology-format

    Elm library providing encoder/decoder for automated slide analysis platform XML format (https://github.com/computationalpathologygroup/ASAP).

    Language:Elm4

  • DeepKernelLearning

    This repository contains code for paper: "Are you sure it’s an artifact? Artifact detection and uncertainty quantification in histological images."

    Language:Python2

  • idc-comppath-reproducibility

    Classification of lung tumor slide images with the NCI Imaging Data Commons

    Language:Jupyter Notebook2

  • TilGenPro

    Python-based pipeline for tiles generation and pre-processing from digitized histopathological images.

    Language:Python2

  • igt-wsi

    Repository for "Integrative Graph-Transformer Framework for Histopathology Whole Slide Image Representation and Classification""

    1

  • CompSegNet

    CompSegNet: An enhanced U-shaped architecture for nuclei segmentation in H&E histopathology images

    Language:Python1

  • Equipping-Computational-Pathology-Systems-with-Artifact-Processing-Pipeline

    computational-pathology-pipeline

    Language:Python1

  • Vision-Transformers-for-Small-Histological-Datasets-Learned-Through-Knowledge-Distillation

    Source code for paper: https://arxiv.org/pdf/2305.17370.pdf

    Language:Python1

  • pathology-cell-density

    A demonstration script for analyzing cell density in whole slide images (WSIs). This repository accompanies the article published on daangeijs.nl. The demo showcases how to compute cell density in detected tumor regions using WholeSlideData and GeoPandas.

    Language:Jupyter Notebook1

  • awesome-pathology

    Awesome List of Digital and Computational Pathology Resources

    1

  • LungEvolutionPathomics

    Lung Preneoplasia Progression via Pathomics

    Language:Python1

  • active-data-enrichment

    [MICCAI'2022] CaPTion workshop: Active Data Enrichment by Learning What to Annotate in Digital Pathology

    1

  • ANSAC

    Classification of whole-slide images based on tumor infiltrating lymphocyte grades using image-level labels

    Language:Python1

  • Reinforcement-Learning-Resources

    Reinforcement learning reading list (including medical image analysis papers )

    1

  • dandyrilla.github.io

    Personal blog on computational biology and pathology

    Language:SCSS1

  • TQx

    Towards a text-based quantitative and explainable histopathology image analysis (MICCAI 2024)