histology

There are 90 repositories under histology topic.

  • qupath/qupath

    QuPath - Open-source bioimage analysis for research

    Language:Java1.1k56825285

  • DigitalSlideArchive/HistomicsTK

    A Python toolkit for pathology image analysis algorithms.

    Language:Python40222304117
  • slideflow

    slideflow/slideflow

    Powerful, open-source AI tools for digital pathology.

    Language:Python2771522648

  • ImagingLab/ICIAR2018

    Two-Stage Convolutional Neural Network for Breast Cancer Histology Image Classification. ICIAR 2018 Grand Challenge on BreAst Cancer Histology images (BACH)

    Language:Python206131476

  • mahmoodlab/HEST

    HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024 (Spotlight)

    Language:Python19544016

  • mahmoodlab/PORPOISE

    Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

    Language:Jupyter Notebook19241437

  • mahmoodlab/TOAD

    AI-based pathology predicts origins for cancers of unknown primary - Nature

    Language:Python17051248

  • axondeepseg/axondeepseg

    Axon/Myelin segmentation using Deep Learning

    Language:Python1161345532

  • DigitalSlideArchive/digital_slide_archive

    The official deployment of the Digital Slide Archive and HistomicsTK.

    Language:Python112169250

  • mahmoodlab/PANTHER

    Morphological Prototyping for Unsupervised Slide Representation Learning in Computational Pathology - CVPR 2024

    Language:Jupyter Notebook10432311

  • mahmoodlab/SISH

    Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering

    Language:Python1004726

  • PolarBean/DeepSlice

    A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

    Language:Python8785219

  • MICA-MNI/micaopen

    Open Scripts and pipelines from the Multimodal Imaging and Connectome Analysis Lab at the Montreal Neurological Institute

    Language:Jupyter Notebook7416340

  • manuel-munoz-aguirre/PyHIST

    A pipeline to segment tissue from the background in histological images

    Language:Python6733013

  • DigitalSlideArchive/HistomicsUI

    A Girder plugin for pathology image annotations and analysis.

    Language:JavaScript581712521

  • yiqings/RandStainNA

    RandStainNA: Simple and efficient augmentations for histology [MICCAI 2022]

    Language:Python521913

  • AIRMEC/im4MEC

    Code for the im4MEC model described in the paper 'Interpretable deep learning model to predict the molecular classification of endometrial cancer from haematoxylin and eosin-stained whole-slide images: a combined analysis of the PORTEC randomised trials and clinical cohorts'.

    Language:Python382513

  • ciccalab/SIMPLI

    SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

    Language:R34655

  • Borda/dataset-histology-landmarks

    Dataset: landmarks for registration of histology images

    Language:Python32618

  • mahmoodlab/CRANE

    Deep learning enabled assessment of cardiac allograft rejection from endomyocardial biopsies- Nature Medicine

    Language:Python28218

  • nauyan/NucleiSegmentation

    The repository contains a simple pipeline for training Nuclei Segmentation Datasets of Histopathology Images.

    Language:Python28114
  • biscuit

    jamesdolezal/biscuit

    Bayesian Inference of Slide-level Confidence via Uncertainty Index Thresholding

    Language:Python27113

  • MWod/ANHIR_MW

    Software used by the AGH team during the ANHIR challenge.

    Language:Python26237

  • MWod/DeepHistReg

    Code used to create the DeepHistReg submission to the ANHIR challenge.

    Language:Python2641115

  • DSLituiev/slideslicer

    a toolbox for manipulation of digital pathology slides and annotations

    Language:Jupyter Notebook19304

  • yiqings/HEGnnEnhanceCnn

    Graph + Image Bimodal Deep Learning for Histology Image Classification

    Language:Python19122

  • BiologyTools/BioImager

    A .NET microscopy imaging application based on Bio library. Supports various microscopes by using imported libraries & GUI automation. Supports XInput game controllers to move stage, take images, run ImageJ macros on images or Bio C# scripts.

    Language:C#13205

  • nmzein/magie

    Analyse gigapixel images, annotated with millions of geometries, using a modern, highly-performant web interface. Built using Rust.

    Language:Rust12251

  • sotiraslab/SC-MIL

    This repo for the paper titled "SC-MIL: Sparsely Coded Multiple Instance Learning for Whole Slide Image Classification"

    Language:Python9320

  • c-arthurs/QuArray

    An application for exporting and analysing tissue array whole slide image files

    Language:Python8104

  • lely475/SoftCTM

    SoftCTM won 3rd place in the OCELOT 2023 Challenge. Multi-organ H&E-based deep learning model for cell detection, applicable for tumor cellularity/ purity/ content estimation.

    Language:Python8120

  • Fouga/SliVo

    2D - 3D slice-to-volume registration pipeline

    Language:MATLAB6110

  • jurgenizer/slidedb

    A virtual slide viewer (virtual microscope) for extremely high-resolution histopathology images. Made with Python, Flask and Leaflet.

    Language:HTML6202

  • xhelenfu/CNN_Segmentation_Histology

    Segmentation of histological images and fibrosis identification with a convolutional neural network

    Language:Python6206
  • slideToolKit

    swvanderlaan/slideToolKit

    slideToolkit: a free toolset for analyzing wholeslide high-resolution digital histological images.

    Language:Shell54171

  • vadori/cytoark

    Processing of histological data for cytoarchitecture analyses.

    Language:Jupyter Notebook5102