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    430 repositories

    • LazySlide

      Public
      Modular and scalable whole slide image analysis
      Python
      •
      MIT License
      •8•0•0•0•Updated Jan 18, 2026Jan 18, 2026

    • GigaTIME

      Public
      Code-base for GigaTIME
      Jupyter Notebook
      •
      Other
      •21•0•0•0•Updated Dec 11, 2025Dec 11, 2025

    • Deep-Learning-Medical-Imaging

      Public
      An end-to-end deep learning pipeline to analyze high-resolution pathology slides by tiling, running inference with PyTorch, and stitching results into an interactive heatmap viewer.
      Jupyter Notebook
      •1•0•0•0•Updated Sep 27, 2025Sep 27, 2025

    • histoplus

      Public
      Python
      •
      Other
      •4•0•0•0•Updated Aug 27, 2025Aug 27, 2025

    • wsianon

      Public
      Whole Slide Images Anonymization Library
      C
      •
      Other
      •1•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • PathQC

      Public
      HTML
      •1•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • ashlar

      Public
      ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
      Python
      •
      MIT License
      •51•0•0•0•Updated Aug 11, 2025Aug 11, 2025

    • TRIDENT

      Public
      Toolkit for large-scale whole-slide image processing.
      Python
      •
      Other
      •101•0•0•0•Updated Jul 13, 2025Jul 13, 2025

    • HistomicsTK

      Public
      A Python toolkit for pathology image analysis algorithms.
      Python
      •
      Apache License 2.0
      •127•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • tiatoolbox

      Public
      Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
      Python
      •
      Other
      •102•0•0•0•Updated Jun 12, 2025Jun 12, 2025

    • Gastritis-MIL-pathology

      Public
      Deep learning for comprehensively assessing chronic gastritis from whole-slide images: a multicenter, retrospective cohort study
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • empaia-integration-wsi-anon

      Public
      copy of https://gitlab.com/empaia/integration/wsi-anon
      C
      •
      MIT License
      •0•1•0•0•Updated Jun 10, 2025Jun 10, 2025

    • GleasonXAI

      Public
      Explainable Gleason pattern prediction.
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Jun 10, 2025Jun 10, 2025

    • pathml

      Public
      Tools for computational pathology
      Python
      •
      GNU General Public License v2.0
      •87•1•0•0•Updated May 24, 2025May 24, 2025

    • path-foundation

      Public
      Python
      •
      Apache License 2.0
      •8•1•0•0•Updated May 19, 2025May 19, 2025

    • STAMP

      Public
      Solid Tumor Associative Modeling in Pathology
      Python
      •
      MIT License
      •46•0•0•0•Updated May 9, 2025May 9, 2025

    • svs-deidentifier

      Public
      Strip potentially identifying label and macro images from Aperio SVS whole slide image files
      Python
      •
      MIT License
      •4•0•0•0•Updated May 8, 2025May 8, 2025

    • wsi-to-dicom-converter

      Public
      Conversion tool/library for converting whole slide images to DICOM
      C++
      •
      Apache License 2.0
      •26•1•0•0•Updated May 1, 2025May 1, 2025

    • NoCodeSeg

      Public
      🔬 Code-free deep segmentation for computational pathology
      Jupyter Notebook
      •
      MIT License
      •16•0•0•0•Updated Apr 26, 2025Apr 26, 2025

    • FAST-Pathology

      Public
      ⚡ Open-source software for deep learning-based digital pathology
      C++
      •
      BSD 2-Clause "Simplified" License
      •25•0•0•0•Updated Apr 26, 2025Apr 26, 2025

    • Midnight

      Public
      Midnight - Pathology foundation models trained on orders of magnitude fewer WSIs
      Python
      •
      MIT License
      •3•1•0•0•Updated Apr 22, 2025Apr 22, 2025

    • AI_handson

      Public
      Realtime prostate cancer segmentation demo
      Jupyter Notebook
      •1•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • MONAILabel

      Public
      MONAI Label is an intelligent open source image labeling and learning tool.
      Python
      •
      Apache License 2.0
      •254•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • DANEELpath

      Public
      Digital Analysis tools for Neuroblastoma Models
      Groovy
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 4, 2025Apr 4, 2025

    • qupath_monaillabel_plugin

      Public
      QuPath - Bioimage analysis & digital pathology
      Java
      •
      GNU General Public License v3.0
      •322•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • UNI

      Public
      Pathology Foundation Model - Nature Medicine
      Jupyter Notebook
      •
      Other
      •82•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • slide2vec

      Public
      WSI feature extraction
      Python
      •7•1•0•0•Updated Mar 17, 2025Mar 17, 2025

    • crc_cells

      Public
      Python
      •1•0•0•0•Updated Mar 16, 2025Mar 16, 2025

    • wsidicom

      Public
      Python package for reading DICOM WSI file sets.
      Python
      •
      Apache License 2.0
      •9•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • SPIDER

      Public
      SPIDER: A multi-organ pathology dataset with expert annotations and pre-trained models for AI-driven research. Available on Hugging Face 🤗.
      Other
      •2•0•0•0•Updated Mar 5, 2025Mar 5, 2025