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    384 repositories

    • TRIDENT

      Public
      Toolkit for large-scale whole-slide image processing.
      Python
      •
      Other
      •6•0•0•0•Updated Feb 13, 2025Feb 13, 2025

    • qupath-extension-wsinfer

      Public
      QuPath extension to work with WSInfer - https://wsinfer.readthedocs.io/
      Java
      •
      Apache License 2.0
      •8•0•0•0•Updated Feb 3, 2025Feb 3, 2025

    • lab-manual

      Public
      The Rendeiro lab manual
      CSS
      •1•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • paquo

      Public
      PAthological QUpath Obsession - QuPath and Python conversations
      Python
      •
      GNU General Public License v3.0
      •18•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • python-zero-to-hero-beginners-course

      Public
      Materials for a Python Beginner's Course. First given at the Royal Society of Biology. Designed and delivered by Chas Nelson and Mikolaj Kundegorski.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •20•0•0•0•Updated Jan 26, 2025Jan 26, 2025

    • QuickAnnotator

      Public
      An open-source digital pathology based rapid image annotation tool
      JavaScript
      •
      BSD 3-Clause Clear License
      •27•0•0•0•Updated Jan 26, 2025Jan 26, 2025

    • HistoQC

      Public
      HistoQC is an open-source quality control tool for digital pathology slides
      JavaScript
      •
      BSD 3-Clause Clear License
      •107•0•0•0•Updated Jan 26, 2025Jan 26, 2025

    • BioImageAnalysisNotebooks

      Public
      Cool
      •
      BSD 3-Clause "New" or "Revised" License
      •37•0•0•0•Updated Jan 26, 2025Jan 26, 2025

    • tiatoolbox

      Public
      Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
      Python
      •
      Other
      •83•0•0•0•Updated Jan 26, 2025Jan 26, 2025

    • dlup

      Public
      Dlup are the Deep Learning Utilities for Pathology developed at the Netherlands Cancer Institute
      Python
      •
      Apache License 2.0
      •7•0•0•0•Updated Jan 26, 2025Jan 26, 2025

    • grandqc

      Public
      GrandQC tool for tissue detection and quality control in pathology
      Python
      •
      Other
      •8•0•0•0•Updated Jan 26, 2025Jan 26, 2025

    • LazySlide

      Public
      Modular and scalable whole slide image analysis
      Python
      •1•0•0•0•Updated Jan 25, 2025Jan 25, 2025

    • wsidata

      Public
      Efficient data structures and IO for whole slide images analysis
      Python
      •1•0•0•0•Updated Jan 25, 2025Jan 25, 2025

    • qupath-extension-gncnn

      Public
      GNCnn (GlomeruloNephritis Classification by neural network): A QuPath extension for glomerulosclerosis and glomerulonephritis characterization based on deep learning
      Java
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Jan 20, 2025Jan 20, 2025

    • dpat_imageanalysisapi_sdk

      Public
      SDK for Sectra's ImageAnalysis API for Digital Pathology
      Python
      •
      BSD 3-Clause Clear License
      •3•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • qupath-docs

      Public
      QuPath documentation
      Python
      •24•0•0•0•Updated Jan 7, 2025Jan 7, 2025

    • TITAN

      Public
      Multimodal Whole Slide Foundation Model for Pathology
      Jupyter Notebook
      •19•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • BiomedParse

      Public
      BiomedParse: A Foundation Model for Joint Segmentation, Detection, and Recognition of Biomedical Objects Across Nine Modalities
      Jupyter Notebook
      •
      Apache License 2.0
      •42•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • qubalab

      Public
      Lab for quantitative bioimage analysis experiments in Python
      Python
      •
      Apache License 2.0
      •4•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • arriba

      Public
      Fast and accurate gene fusion detection from RNA-Seq data
      C++
      •
      Other
      •51•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • multiview-stitcher

      Public
      A toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •8•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • instanseg

      Public
      Python
      •
      Apache License 2.0
      •21•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • i2k2024

      Public
      Groovy
      •2•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • DigiPathoImageAnalysis

      Public
      List of academic institutes/companies working on computer-based digital pathology image analysis
      11•0•0•0•Updated Oct 26, 2024Oct 26, 2024

    • hibou

      Public
      Hibou: Foundational Models for Pathology
      Python
      •
      Apache License 2.0
      •7•0•0•0•Updated Oct 23, 2024Oct 23, 2024

    • wsinfer

      Public
      🔥🚀 Blazingly fast pipeline for patch-based classification in whole slide images
      Python
      •
      Apache License 2.0
      •12•1•0•0•Updated Oct 21, 2024Oct 21, 2024

    • qupath-extension-sam

      Public
      QuPath extension for Segment Anything Model (SAM)
      Java
      •
      GNU General Public License v3.0
      •15•1•0•0•Updated Oct 19, 2024Oct 19, 2024

    • samapi

      Public
      Segment Anything Model API
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •14•0•0•0•Updated Oct 19, 2024Oct 19, 2024

    • digitalsreeni-image-annotator

      Public
      A python based GUI to annotate images and save annotations as COCO style JSON format.
      Python
      •
      Other
      •28•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • fseg

      Public
      Unsupervised Semantic Segmentation for Pathology
      Jupyter Notebook
      •
      Apache License 2.0
      •4•0•0•0•Updated Oct 16, 2024Oct 16, 2024