whole-slide-imaging

There are 12 repositories under whole-slide-imaging topic.

qupath / qupath
QuPath - Bioimage analysis & digital pathology
bioimage-informatics image-processing digital-pathology pathology machine-learning cell-segmentation whole-slide-imaging bioimage-analysis cell-analysis imagej opencv groovy histology javafx tissue-microarray-analysis computational-pathology
Language:Java 1007
CLAM
mahmoodlab / CLAM
Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
histopathology pathology weakly-supervised-learning whole-slide-imaging data-efficient computational-pathology mahmoodlab bioimage-informatics deep-learning tcga-data camelyon16 camelyon17 clam digital-pathology quantitative-pathology
Language:Python 974
baidu-research / NCRF
Cancer metastasis detection with neural conditional random field (NCRF)
deep-learning conditional-random-fields pathology whole-slide-imaging camelyon16
Language:Python 751
computationalpathologygroup / ASAP
Program for the analysis and visualization of whole-slide images in digital pathology
computation-pathology whole-slide-imaging
Language:C++ 602
cgohlke / tifffile
Read and write TIFF files
format-reader image imagej life-sciences-image numpy ome-tiff python tiff whole-slide-imaging zarr
Language:Python 507
openslide / openslide
C library for reading virtual slide images
c pathology whole-slide-imaging
Language:C 397
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-formats format-converter format-reader image java life-sciences-image lightsheet metadata whole-slide-imaging wsi
Language:Java 375
TissueImageAnalytics / tiatoolbox
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
python computational-pathology whole-slide-imaging deep-learning digital-pathology histopathology image-analysis machine-learning tissue-analysis tissue-segmentation cell-classification cell-segmentation medical-image-analysis stain-normalization
Language:Python 345
binli123 / dsmil-wsi
DSMIL: Dual-stream multiple instance learning networks for tumor detection in Whole Slide Image
deep-learning multiple-instance-learning whole-slide-imaging whole-slide-image tumor-detection self-attention weakly-supervised-learning histopathology deep-neural-networks semi-supervised-learning self-supervised-learning pytorch transformer visiontransformer
Language:Python 336
slideflow
jamesdolezal / slideflow
Deep learning library for digital pathology, with both Tensorflow and PyTorch support.
python machine-learning deep-learning pathology histology computational-pathology whole-slide-imaging histopathology
Language:Python 235
camicroscope / caMicroscope
Digital pathology image viewer with support for human/machine generated annotations and markups.
whole-slide-imaging digital-pathology camicroscope slide-images
Language:JavaScript 233
nadeemlab / DeepLIIF
Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]
ai-ready cell-biology cell-segmentation cloud-native-applications datasets deep-learning digital-pathology image-segmentation immunohistochemical-images immunohistochemistry multiplex multitask-learning pathology pathology-gan pathology-image pytorch segmentation stitching super-resolution whole-slide-imaging
Language:Python 151
MarvinLer / tcga_segmentation
Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024
multiple-instance-learning image-segmentation histopathology tumor-segmentation whole-slide-imaging wsi miccai tcga slide-image-segmentation tcga-data weakly-supervised-learning pathology computational-pathology data-efficient medical-imaging segmentation
Language:Python 114
ChongQingNoSubway / PDL
Code for the paper " PDL: Regularizing Multiple Instance Learning with Progressive Dropout Layers "
multiple-instance-learning histopathology histopathology-image-analysis histopathology-images tumor-detection weakly-supervised-learning whole-slide-image whole-slide-imaging
Language:Python 113
cylab-tw / bluelight
a browser-based DICOM viewer
dicom dicomweb html5 bluelight dicom-web-viewer dicom-viewer orthanc dicom-server rtss dicom-overlay wsi whole-slide-imaging
Language:JavaScript 103
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.
histopathology iterator whole-slide-image whole-slide-annotation pathology python whole-slide-imaging deep-learning wsa wsi wsm whole-slide-mask wsd whole-slide-dataset whole-slide-data computational-pathology
Language:Python 86
btcrabb / SlideSeg
A Python module that produces image patches and annotation masks from whole slide images for deep learning in digital pathology.
digital-pathology semantic-segmentation whole-slide-imaging convolutional-neural-networks
Language:Jupyter Notebook 78
cytomine / Cytomine-core
Cytomine-Core is the main web server implementing the Cytomine API
cytomine digital-pathology machine-learning whole-slide-imaging computational-pathology
Language:Groovy 70
YashSharma / C2C
Implementation of Cluster-to-Conquer: A Framework for End-to-End Multi-Instance Learning for Whole Slide Image Classification approach.
deep-learning histopathology multiple-instance-learning weakly-supervised-learning whole-slide-imaging
Language:Python 59
jgamper / compay-syntax
:microscope: Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.
computational-pathology medical-imaging wsis openslide slide-images pathology-image whole-slide-image whole-slide-imaging
Language:Python 55
SBU-BMI / wsinfer
🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images
deep-learning pathology whole-slide-imaging pytorch classification
Language:Python 55
DeepMicroscopy / Exact
An open source online platform for collaborative image labeling of almost everything
algorithm-aided collaboration annotations whole-slide-imaging version-control
Language:JavaScript 54
PingjunChen / pyslide
Digital Pathology Whole Slide Image Analysis Toolbox
pathology whole-slide-imaging deep-learning python image-analysis computational-pathology
Language:Python 48
lucasrla / wsi-preprocessing
Simple library for preprocessing histopathological whole-slide images (WSI) into tiles (a.k.a. patches) towards deep learning
fastai histopathology libvips openslide pathology preprocessing pytorch pyvips whole-slide-imaging wsi
Language:Python 45
PingjunChen / tissueloc
Whole Slide Digital Pathology Image Tissue Localization
whole-slide-imaging pathology computational-pathology pathology-image tissue-localization python
Language:Python 44
WonderLandxD / sdpc-for-python
Python library for processing whole slide images (WSIs) in sdpc format
python whole-slide-imaging sdpc-format
Language:Python 32
liupei101 / Pipeline-Processing-TCGA-Slides-for-MIL
This repo provides an exhaustive pipeline of processing TCGA whole-slide images for downstream multiple instance learning.
histopathology-image-analysis multiple-instance-learning tcga whole-slide-imaging
Language:Python 29
mahmoodlab / CRANE
Deep learning enabled assessment of cardiac allograft rejection from endomyocardial biopsies- Nature Medicine
biopsy-screening endomyocardial histology pathology weakly-supervised-learning whole-slide-imaging
Language:Python 28
biscuit
jamesdolezal / biscuit
Bayesian Inference of Slide-level Confidence via Uncertainty Index Thresholding
computational-pathology deep-learning histology machine-learning pathology whole-slide-imaging uncertainty-quantification
Language:Python 25
lucasrla / wsi-tile-cleanup
Image filters for digital pathology: detect pen marks, background, and artifacts. Use them for preprocessing towards deep learning
deep-learning fastai histopathology libvips otsu-threshold pathology preprocessing pytorch pyvips whole-slide-imaging wsi
Language:Python 24
koriavinash1 / DigitalHistoPath
histopathology digital-pathology whole-slide-imaging deep-learning uncertainty-quantification digestpath paip camelyon16 camelyon camelyon17 segmentation-models
Language:Jupyter Notebook 23
DIMAthe47 / slide_viewer_47
A pyqt5 widget for viewing whole-slide images with Openslide
whole-slide-imaging openslide pyqt5 python3
Language:Python 21
tand826 / wsiprocess
Whole Slide Image (WSI) Processing Library for Histopathological / Cytopathological Machine Learning Tasks
histopathology cytopathology medical-imaging whole-slide-imaging machine-learning wsi
Language:Python 20
uw-loci / demo_wsi_superres
WSISR: Single image super-resolution for Whole slide Imaging using convolutional neural networks and self-supervised color normalization.
whole-slide-imaging histopathology super-resolution whole-slide-image convolutional-neural-networks generative-adversarial-network deep-learning self-supervised-learning curriculum-learning single-image-super-resolution
Language:Python 20
liupei101 / DSCA
[ESWA 2023] Implementation of DSCA: A Dual-stream Network with Cross-attention on Whole-Slide Image Pyramids for Cancer Prognosis
cancer-prognosis dual-stream survival-analysis whole-slide-imaging wsi-images
Language:Python 19
GoogleCloudPlatform / qupath-chcapi-extension
Extension to QuPath application adding support for reading from Google Cloud Healthcare API.
dicom dicomweb whole-slide-imaging
Language:Java 18