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    375 repositories

    • TITAN

      Public
      Multimodal Whole Slide Foundation Model for Pathology
      Jupyter Notebook
      •16•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
      •32•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • dpat_imageanalysisapi_sdk

      Public
      SDK for Sectra's ImageAnalysis API for Digital Pathology
      BSD 3-Clause Clear License
      •3•0•0•0•Updated Nov 25, 2024Nov 25, 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
      •20•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
      •24•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

    • qupath-extension-instanseg

      Public
      The official QuPath extension for InstanSeg
      Java
      •
      Apache License 2.0
      •6•0•0•0•Updated Oct 16, 2024Oct 16, 2024

    • opentile

      Public
      Python library for reading tiles from wsi tiff-files.
      Python
      •
      Apache License 2.0
      •4•0•0•0•Updated Oct 10, 2024Oct 10, 2024

    • slideio

      Public
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•0•0•Updated Oct 5, 2024Oct 5, 2024

    • FrOoDo

      Public
      Jupyter Notebook
      •
      MIT License
      •7•0•0•0•Updated Oct 3, 2024Oct 3, 2024

    • HistoQC

      Public
      HistoQC is an open-source quality control tool for digital pathology slides
      JavaScript
      •
      BSD 3-Clause Clear License
      •106•0•0•0•Updated Sep 28, 2024Sep 28, 2024

    • VoltRon

      Public
      Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration
      R
      •
      Other
      •10•0•0•0•Updated Sep 23, 2024Sep 23, 2024

    • Awesome-Polyp-Segmentation

      Public
      16•0•0•0•Updated Sep 21, 2024Sep 21, 2024

    • predictive_biomarker_collagen_dcis

      Public
      Collagen biomarker predictive of tamoxifen benefit in DCIS
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Aug 23, 2024Aug 23, 2024

    • SAM2PATH

      Public
      SAM2PATH paper code repo
      Python
      •2•0•0•0•Updated Aug 8, 2024Aug 8, 2024

    • tissue_segmentation

      Public
      This script takes whole slide images (typically .svs or .ndpi files; either from biospsies or Cytosponge etc) as an input and returns an image file (typically .png file) of the mask of where the tissue is located (black: tissue, white: background).
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 22, 2024Jul 22, 2024

    • ISGPP-model

      Public
      Model Weights for the ISGPP model for the segmentation of Pancreatic Ductal Adenocarcinoma (PDAC) after neoadjuvant therapy
      1•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • PatchSorter

      Public
      A tool for rapidly labeling objects using deep learning feature embedding
      JavaScript
      •
      BSD 3-Clause Clear License
      •10•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • nuclei.io

      Public
      nuclei.io: Human-in-the-loop active learning framework for pathology image analysis
      Python
      •
      MIT License
      •11•0•0•0•Updated Jun 19, 2024Jun 19, 2024

    • omnipose

      Public
      Omnipose: a high-precision solution for morphology-independent cell segmentation
      Jupyter Notebook
      •
      Other
      •32•0•0•0•Updated Apr 30, 2024Apr 30, 2024

    • qupath-extension-cellpose

      Public
      an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.
      Jupyter Notebook
      •
      Apache License 2.0
      •11•0•0•0•Updated Apr 30, 2024Apr 30, 2024