openslide

There are 2 repositories under openslide topic.

• libvips / libvips

  A fast image processing library with low memory needs.

  ccppgifgraphicsmagickheicimage-processingimagemagickjpeglibvipsniftiopenexropenslidepdfpdfiumpngsvgtiffwebp
  Language:C 10650

• ysbecca / py-wsi

  Python package for dealing with whole slide images (.svs) for machine learning, particularly for fast prototyping. Includes patch sampling and storing using OpenSlide. Patches may be stored in LMDB, HDF5 files, or to disk. It is highly recommended to fork and download this repository so that personal customisations can be made for your work.

  openslidepy-wsiopenslide-pythonlmdbsvsdeep-learning
  Language:Jupyter Notebook 161

• GoogleCloudPlatform / wsi-to-dicom-converter

  Conversion tool/library for converting whole slide images to DICOM

  dicomwsiopenslide
  Language:C++ 82

• 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 71

• zhaoxuanma / Deeplearning-digital-pathology

  Full package for applying deep learning to virtual slides.

  caffedeep-learningdigital-pathologykerasopenslidetensorflow
  Language:Python 68

• jgamper / compay-syntax

  :microscope: Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.

  computational-pathologymedical-imagingwsisopenslideslide-imagespathology-imagewhole-slide-imagewhole-slide-imaging
  Language:Python 55

• 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 52

• smujiang / WSITools

  Tools for whole slide image (WSI) processing. Especially for (pairwise) patch extraction, annotation parsing and data preparation for deep learning purposes.

  digital-pathologyextractionimage-processingopenslidepatchpathologicalwis
  Language:Python 49

• DIMAthe47 / slide_viewer_47

  A pyqt5 widget for viewing whole-slide images with Openslide

  openslidepyqt5python3whole-slide-imaging
  Language:Python 22

• jopo666 / HistoPrep

  Preprocessing module for large histological images

  openslidepathologypathology-imagetissue-classificationtissue-analysishistological-imagesmedical-imagingmedical-image-processingmedical-image-analysishistological-slidesslide-imagepreprocesscut
  Language:Python 20

• DSLituiev / slideslicer

  a toolbox for manipulation of digital pathology slides and annotations

  openslidewsiannotationsmaskpathologyhistologyslideslicertissueread-slides
  Language:Jupyter Notebook 19

• andreped / vsi2tif

  Simple tool for converting WSIs from cellSens VSI to pyramidal TIFF

  wsiolympuscellsensvsitiftiffpyramidalconverterbioformatsfastgenericopenslidepyvipsvipsbftoolscucimpyfast
  Language:Jupyter Notebook 18

• deephealthproject / ecvl

  European Computer Vision Library (ECVL). A general-purpose computer vision library developed to support healthcare use cases within the DeepHealth project, with the aim of facilitating the integration of existing state-of-the-art libraries.

  computer-graphicscomputer-visioncppdicomecvlfpga-accelerationgpu-accelerationimage-processingopenslide
  Language:C++ 17

• steven22tom / LabelSlide

  LabelSlide is a slide annotation tool and label object bounding boxes in virtual slides (generally used in pathology)

  labeltoolopenseadragonopenslidedigital-pathologypathologypathology-imageannotationsdeep-learningpython3
  Language:JavaScript 16

• girder / large_image_wheels

  manylinux wheel files for girder/large_image dependencies

  binarygdallibtifflibvipsmapnikopenslideopenslide-pythonpyprojpyvipswheelsglymurpylibtiffpython-javabridge
  Language:Dockerfile 14

• BiologyTools / BioGTK

  A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.

  bio-formatsbiologygtkimage-stacksimagejmicroscopyroicross-platformomeroimagej-roiimagej-tiffwhole-slide-imagesegment-anythingsegment-anything-modelopenslidepluginsgeojsonqupathsam-2
  Language:C# 12

• hurryhuang1007 / Xslide

  An application that can quickly view large images like .tif, .svs, .bif, .hdpi, .vms and .mrxs file(s).

  vipsopenslideviewertifsvsvmsmrxshdpideep-zoom-images
  Language:JavaScript 11

• InsightSoftwareConsortium / ITKIOOpenSlide

  An ITK ImageIO module for the OpenSlide library.

  itk-moduleopenslideopenslide-pythonmicroscopy
  Language:C++ 11

• shaziaakbar / deep-openslide

  A library for training deep neural networks using pathology data by accessing patches on-the-fly

  pathologyopenslide
  Language:Python 6
• slideToolKit

  swvanderlaan / slideToolKit

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

  histologycellprofileropenslide
  Language:Shell 5

• jammy-dodgers / gophenslide

  Unofficial Go bindings for OpenSlide - I don't like Go, by the way.

  openslide
  Language:Go 4

• yujota / openslider-tfpy

  TensorFlow cunstom runner to read micro images from whole slide images.

  openslidepathologytensorflowwsi
  Language:Jupyter Notebook 4
• 3Dhistopathology

  agam-kashyap / 3Dhistopathology

  3D visualisation using Inviwo and OpenSlide

  inviwo3d-histopathologydvrvolume-ray-castingopenslide
  Language:C++ 3

• arquolo / bipl

  Big Image Python Library

  computer-visionimage-processingopenslidepythontiff
  Language:Python 3

• BioImageInformatics / svs_reader

  Convenient interface for generating tiles from Aperio SVS format images

  svsopenslideopencvdigital-pathologyaperiotensorflowtensorflow-data-pipeline
  Language:Python 3

• DIMAthe47 / slide_list_view_47

  A pyqt5 widget for viewing collection of whole-slide images with Openslide

  pyqt5python3listviewwhole-slide-imagingopenslide
  Language:Python 3
• TensorBoard_Plugin_WSI

  IAmS4n / TensorBoard_Plugin_WSI

  A plugin for TensorBoard to show WSI images. The plugin is based on Deep Zoom Image (DZI).

  deepzoomdzihistopathologyopenslideplugintensoflowtensorboardviewervisualizationwsiwsi-imageswsi-viewer
  Language:JavaScript 3

• leesei / openslide-prop2json

  Parse OpenSlide properties (generated by `openslide-show-properties`) to JSON

  openslidejson
  Language:JavaScript 3

• DIMAthe47 / slide_cbir_47

  A pyqt5 GUI for CBIR in whole-slide images with Openslide

  whole-slide-imagingopenslidepyqt5python3cbir
  Language:Python 2

• Mudit219 / 3Dhistopathology

  3D visualisation using Inviwo and OpenSlide

  cpp14openslide
  Language:C++ 2

• AnirbitGhosh / L4-Project

  Project title: Using Deep Learning to predict overall survival times for breast cancer from H&E whole slide biopsy

  convolutional-neural-networksdeep-learninghistopathology-image-analysismachine-learningopenslidepythonpytorch
  Language:TeX 1

• Anivader / CPATH

  This codebase provides computational pipelines for implementing Deep Learning-assisted Whole Slide Image (WSI) classification

  deep-learninggpu-accelerationimage-proimageioopencv-pythonopenslidepython-3pytorch-implementationscikit-imagecomputational-pa
  Language:Jupyter Notebook 1

• brian220 / SvsScanner

  Use the openslide Library to process the WSI image

  wsi-imagesopenslide
  Language:Python 1

• Dart9000 / OpenX

  Digital Open-source pathology tool based on OpenSlide with Manipulation & annotations feature.

  openslideopenseadragonannotationopenseadragon
  Language:Python 1

• VanAndelInstitute / svs2vsv

  Process Aperio SVS images in S3 with vips/openslide.

  aperiosvsvipsopenslide
  Language:Dockerfile 1

• yjg30737 / pyqt-wsi-viewer

  PyQt WSI(Whole Slide Images) viewer

  openslidepyqtpyqt5pyqt5-desktop-applicationpythonqtwsi
  Language:Roff 1