wsi

There are 1 repository under wsi topic.

• BMIRDS / deepslide

  Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

  histopathology-imagesmicroscopysliding-windowsmedical-image-analysisresnetwsilungcancerpathology-image
  Language:Python 480

• ome / bioformats

  Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

  bio-formatsjavaimagelife-sciences-imageformat-readerformat-convertermetadatawhole-slide-imagingwsilightsheet
  Language:Java 376

• histolab / histolab

  Library for Digital Pathology Image Processing

  bioinformaticsbiologydata-sciencedigital-pathologydigital-pathology-datahacktoberfestpathologypythonresearchscience-researchwsi
  Language:Python 355

• MarvinLer / tcga_segmentation

  Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024

  multiple-instance-learningimage-segmentationhistopathologytumor-segmentationwhole-slide-imagingwsimiccaitcgaslide-image-segmentationtcga-dataweakly-supervised-learningpathologycomputational-pathologydata-efficientmedical-imagingsegmentation
  Language:Python 118

• mahmoodlab / Patch-GCN

  Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks - MICCAI 2021

  wsiwsi-imagesgcnsurvival-predictionpathologyhistopathologymahmoodlab
  Language:Python 114

• cylab-tw / bluelight

  a browser-based DICOM viewer

  dicomdicomwebhtml5bluelightdicom-web-viewerdicom-viewerorthancdicom-serverrtssdicom-overlaywsiwhole-slide-imaging
  Language:JavaScript 113

• DIAGNijmegen / pathology-whole-slide-data

  A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.

  histopathologyiteratorwhole-slide-imagewhole-slide-annotationpathologypythonwhole-slide-imagingdeep-learningwsawsiwsmwhole-slide-maskwsdwhole-slide-datasetwhole-slide-datacomputational-pathology
  Language:Python 89

• GoogleCloudPlatform / wsi-to-dicom-converter

  Conversion tool/library for converting whole slide images to DICOM

  dicomopenslidewsi
  Language:C++ 74

• haranrk / DigiPathAI

  Tool to visualize gigantic pathology images and use AI to segment cancer cells and present as an overlay

  deep-learningcancer-researchsegmentationguimedical-image-analysisopenslidepythonwsi
  Language:JavaScript 64

• manuel-munoz-aguirre / PyHIST

  A pipeline to segment tissue from the background in histological images

  histological-imageshistologysegmentationsvsimage-segmentationcomputational-pathologyhistopathologywsi
  Language:Python 62
• raccoon

  cylab-tw / raccoon

  Raccoon is a NoSQL-based medical image archive for managing the DICOM images.

  dicomwebfhir-servermongodbfhir-resourceswado-urifhir-imagingstudyqido-rspathologywsibluelight
  Language:JavaScript 50

• lucasrla / wsi-preprocessing

  Simple library for preprocessing histopathological whole-slide images (WSI) into tiles (a.k.a. patches) towards deep learning

  libvipspyvipsopenslidewhole-slide-imagingwsipathologypreprocessingfastaipytorchhistopathology
  Language:Python 45

• GoogleCloudPlatform / dicomweb-wsi-viewer

  Proof of concept whole slide imaging viewer on top of Google Cloud Healthcare DICOM API.

  dicomdicomwebwsi
  Language:JavaScript 38
• mil4wsi

  aimagelab / mil4wsi

  DAS-MIL: Distilling Across Scales for MILClassification of Histological WSIs

  milwsi
  Language:Python 37

• tcxxxx / WSI-analysis

  Python scripts for automatic Whole-Slide Image preprocessing.

  medicalwholeslide-imagingwsipatchesmultipleinstanceimageprocessing
  Language:HTML 35

• asafamr / bertwsi

  Word Sense Induction with BERT MLM

  wsiword-sense-inductionword-sense-disambiguationbert
  Language:Python 28
• kat

  Zhengyushan / kat

  The code for Kernel attention transformer (KAT)

  whole-slide-imagehistopathologyhistopathology-imageshistopathology-wsiwsiwsi-imageswsi-classificaitonwsi-representationpathology-imagewsi-encodehistopathology-featurehistopathology-image-classficationkernel-transformer
  Language:Python 26

• lucasrla / wsi-tile-cleanup

  Image filters for digital pathology: detect pen marks, background, and artifacts. Use them for preprocessing towards deep learning

  deep-learningfastaihistopathologylibvipsotsu-thresholdpathologypreprocessingpytorchpyvipswhole-slide-imagingwsi
  Language:Python 25

• Jonas1312 / PFA-ScanNet

  PFA-ScanNet: Pyramidal Feature Aggregation With Synergistic Learning for Breast Cancer Metastasis Analysis (Architecture Only Pytorch Implementation).

  breastcamelyoncamelyon16camelyon17cancerpfapfa-scannetscannetwsi
  Language:Python 22

• tand826 / wsiprocess

  Whole Slide Image (WSI) Processing Library for Histopathological / Cytopathological Machine Learning Tasks

  histopathologycytopathologymedical-imagingwhole-slide-imagingmachine-learningwsi
  Language:Python 21

• DSLituiev / slideslicer

  a toolbox for manipulation of digital pathology slides and annotations

  openslidewsiannotationsmaskpathologyhistologyslideslicertissueread-slides
  Language:Jupyter Notebook 19

• cpystan / Wsi-Caption

  Official Inplementation of 《WsiCaption: Multiple Instance Generation of Pathology Reports for Gigapixel Whole Slide Images》(MICCAI 2024)

  aigcpathologypythonvisual-languagewsi
  Language:Python 17
• CytoBrowser

  MIDA-group / CytoBrowser

  CytoBrowser, a JavaScript and Node.js driven environment for fast and accessible collaborative online visualization, assessment, and annotation of very large microscopy images.

  cytologycytopathologywsiwhole-slide-imagingannotationsannotation-layerjavascriptmachine-learningwebappmicroscopy-imagesvisualizationnodejsnode-jsdeep-learning
  Language:JavaScript 16

• constantjxyz / GC-SPLeM

  Survival Prediction for Gastric Cancer via Multimodal Learning of Whole Slide Images and Gene Expression -- BIBM 2022

  gene-expressiongraph-convolutional-networkmultimodal-learningsurvival-predictionwsi
  Language:Python 15

• yasohasakii / WSI-SDK

  Toolkit for WSI preprocess, such as resample & zoom, mask, roi selection ect.

  wsi
  Language:Python 15

• smujiang / WSI2DICOM

  Simple prototype of converting whole slide image (WSI) to multiframe DICOM images

  wsidicomconvertsvsimage-formatimage-format-conversionimage-format-converterpathology-image
  Language:Python 14

• andreped / vsi2tif

  Simple method for converting the CellSens .vsi format to a pyramidal .tif

  wsiolympuscellsensvsitiftiffpyramidalconverter
  Language:Python 11

• ysbecca / fwat

  A Fast Whole-slide image Annotation Tool (FWAT) for conducting painless studies requiring annotations on whole-slide images.

  annotationsflaskpythonwhole-slide-imagingwsi
  Language:JavaScript 11

• Katalip / ca-stinv-cnn

  Code for "Improving Stain Invariance of CNNs for Segmentation by Fusing Channel Attention and Domain-Adversarial Training"

  cnnconvnetdistribution-shiftinvariancesemantic-segmentationwsi
  Language:Python 10

• PingjunChen / ThyroidInteractive

  Suspicious Regions-Based Whole Slide Image Analysis

  wsisuspicious-regioncomputer-aided-diagnosisdeep-representationretrievaldeep-learningcomputational-pathology
  Language:Python 10
• ThyroidRule

  PingjunChen / ThyroidRule

  Rule-Based Thyroid Whole Slide Image Diagnosis

  wsithyroid-cancerrule-basedcnn-classificationpatch-wiseconvolutional-neural-networksdeep-learningdeep-neural-networkspytorchcomputational-pathology
  Language:Python 10

• uzunb / deep-zoom-image-viewer

  This is a viewer app that provides using to zoom and pan tools Deep Zoom Image (dzi) or Whole Slide Image (wsi) using Electron JS and OpenSeaDragon .

  deep-zoom-imagesdzielectronelectron-appelectronjsnodenode-jsnodejsopenseadragonopenseadragon-viewerwhole-slide-imagewhole-slide-imagingwsiwsi-images
  Language:JavaScript 10

• c-arthurs / labelstrip

  GUI wrapped around anonymise label for SVS and NDPI whole slide images

  wsiwhole-slide-imagingsvsndpilabelslideslide-labelannonymized
  Language:Python 9

• UESTC-nnLab / ProDiv

  [CMPB 2024] ProDiv: Prototype-driven consistent pseudo-bag division for whole-slide image classification

  classificationmultiple-instance-learningwhole-slide-imagingwsi
  Language:Python 7

• Zhengyushan / lagenet

  The code for LAGE-Net

  histopathology-imageshistopathology-image-analysiswsiwhole-slide-imagehistopathology-image-retrieval
  Language:Python 7

• skoc / wsi-heatmap

  WSI Clustering Heatmap with ResNet Features

  heatmapwsiclusteringfeature-extractionself-supervised-learning
  Language:Python 5