digital-pathology

There are 20 repositories under digital-pathology 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 971
FAST
smistad / FAST
A framework for high-performance medical image processing, neural network inference and visualization
opencl visualization parallel-computing medical-imaging gpu-computing deep-learning streaming ultrasound digital-pathology image-processing python
Language:C++ 403
pathml
Dana-Farber-AIOS / pathml
Tools for computational pathology
machine-learning digital-pathology computational-pathology biomedical-image-processing pathology histopathology spatial-transcriptomics image-analysis microscopy fluorescence-microscopy-imaging deep-learning python pytorch research pathml
Language:Python 361
histolab / histolab
Library for Digital Pathology Image Processing
digital-pathology-data digital-pathology bioinformatics biology wsi hacktoberfest data-science python science-research research pathology
Language:Python 338
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 318
rapidsai / cucim
cuCIM - RAPIDS GPU-accelerated image processing library
image-processing computer-vision medical-imaging microscopy digital-pathology cuda gpu nvidia image-analysis image-data segmentation multidimensional-image-processing
Language:Jupyter Notebook 307
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 224
AICAN-Research / FAST-Pathology
⚡ Open-source software for deep learning-based digital pathology
deep-learning machine-learning digital-pathology computational-pathology software free-to-use opencl opengl tensorrt openvino pytorch cplusplus tensorflow inference deployment convolutional-neural-networks fastpathology
Language:C++ 114
ImagingDataCommons / slim
Interoperable web-based slide microscopy viewer and annotation tool
dicomweb oidc react digital-pathology idc-viewers
Language:TypeScript 108
EIDOSLAB / torchstain
Stain normalization tools for histological analysis and computational pathology
pytorch histopathology stain-normalization computational-pathology medical-imaging python digital-pathology numpy tensorflow
Language:Python 100
Bayer-Group / paquo
PAthological QUpath Obsession - QuPath and Python conversations
digital-pathology python qupath
Language:Python 97
AdalbertoCq / Pathology-GAN
Corresponding code of 'Quiros A.C., Murray-Smith R., Yuan K. Pathology GAN: Learning deep representations of cancer tissue. Proceedings of The 3rd International Conference on Medical Imaging with Deep Learning (MIDL) 2020'
gans generative-adversarial-network representation-learning pathology-gan digital-pathology histopathology
Language:Python 88
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
Bayer-Group / tiffslide
TiffSlide - cloud native openslide-python replacement based on tifffile
digital-pathology python
Language:Python 74
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
zhaoxuanma / Deeplearning-digital-pathology
Full package for applying deep learning to virtual slides.
deep-learning digital-pathology keras caffe openslide tensorflow
Language:Python 66
SSL_CR_Histo
srinidhiPY / SSL_CR_Histo
Official code for "Self-Supervised driven Consistency Training for Annotation Efficient Histopathology Image Analysis" Published in Medical Image Analysis (MedIA) Journal, Oct, 2021.
self-supervised-learning digital-pathology camelyon16 breastpathq teacher-student-training annotation-efficient semi-supervised-learning deep-learning histopathology
Language:Python 62
okunator / cellseg_models.pytorch
Encoder-Decoder Cell and Nuclei segmentation models
accelerate ai cell-segmentation cellpose digital-pathology hovernet microscopy ml nuclei-segmentation omnipose panoptic-segmentation pytorch pytorch-lightning stardist tissue-segmentation timm
Language:Python 61
andreped / NoCodeSeg
🔬 Code-free deep segmentation for computational pathology
deep-learning u-net fastpathology deepmib qupath digital-pathology open-datasets open-annotations convolutional-neural-networks semantic-segmentation multi-class annotation cpp matlab java medical-imaging
Language:Jupyter Notebook 45
icbcbicc / FocusLiteNN
Official PyTorch and MATLAB implementations of our MICCAI 2020 paper "FocusLiteNN: High Efficiency Focus Quality Assessment for Digital Pathology"
image-processing digital-pathology deep-learning deep-neural-networks convolutional-neural-network medical-image-processing image-quality-assessment network-distillation pathological-images pytorch
Language:Python 38
dazhangyu123 / ACMIL
WSI classification
bracs camelyon16 computational-pathology digital-pathology multiple-instance-learning pathology-image whole-slide-image acmil weakly-supervised-learning histopathology
Language:Python 33
Zhengyushan / adaptive_color_deconvolution
adaptive color deconvolution for paper "Zheng et al., CMPB, 2019"
digital-pathology stain-normalization stain-separation stain-standardization color-normalization histological-images histopathological-image
Language:Python 32
smujiang / WSITools
Tools for whole slide image (WSI) processing. Especially for (pairwise) patch extraction, annotation parsing and data preparation for deep learning purposes.
pathological image-processing wis patch extraction openslide digital-pathology
Language:Python 29
imi-bigpicture / wsidicom
Python package for reading DICOM WSI file sets.
annotations dicom digital-pathology whole-slide-image
Language:Python 28
koriavinash1 / DigitalHistoPath
histopathology digital-pathology whole-slide-imaging deep-learning uncertainty-quantification digestpath paip camelyon16 camelyon camelyon17 segmentation-models
Language:Jupyter Notebook 23
rikiyay / style-transfer-for-digital-pathology
Learning domain-agnostic visual representation for computational pathology using medically-irrelevant style transfer augmentation
computer-vision representation-learning style-transfer computational-pathology digital-pathology data-augumentation deep-learning
Language:Python 21
TissUUmapsCore
TissUUmaps / TissUUmapsCore
TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer, and allows users to share regions of interest and local statistics.
bioinformatics computational biology gene-expression gene-expression-profiles digital-pathology
Language:JavaScript 20
AICAN-Research / H2G-Net
🚀 H2G-Net: Segmentation of breast cancer region from whole slide images
h2g-net cnn tensorflow-keras digital-pathology computational-pathology u-net agu-net mobilenetv2 breast-cancer clustering convolutional-neural-networks medical-imaging refinement segmentation whole-slide-image deep-learning tensorflow
Language:TeX 19
andreped / fast-stain-normalization
:star2: GPU-accelerated stain normalization command line tool
histopathology-images digital-pathology stain-normalization deep-learning cpp python computational-pathology fast torch tensorflow tensorflow2
Language:Python 19
Bayer-Group / pado
PAthological Data Obsession - cloud native digital pathology datasets
python digital-pathology
Language:Python 17
srinidhiPY / ICCV-CDPATH2021-ID-8
Official code for "Improving Self-supervised Learning with Hardness-aware Dynamic Curriculum Learning: An Application to Digital Pathology", ICCV, 2021, CDpath Workshop (Oral).
self-supervised-learning curriculum-learning digital-pathology deep-learning
Language:Python 17
smujiang / WSIPenMarkingRemoval
Remove pen-marking annotations on whole slide images(WSIs) for data achiving.
image-normalization deep-learning digital-pathology gan image-inpainting image-restoration
Language:Python 15
steven22tom / LabelSlide
LabelSlide is a slide annotation tool and label object bounding boxes in virtual slides (generally used in pathology)
labeltool openseadragon openslide digital-pathology pathology pathology-image annotations deep-learning python3
Language:JavaScript 15
PathologyDataScience / HiPS
Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
biomarker-discovery biomedical-image-processing breast-cancer computational-pathology digital-pathology survival-prediction explainable-ai
Language:Python 14
CielAl / torch-staintools
Pytorch-adaptation of GPU-accelerated StainTool's stain normalization algorithms
pytorch reinhard stain-normalization macenko staintools vahadane computational-pathology digital-pathology gpu-acceleration stain-augmentation pytorch-staintools stain-separation
Language:Python 13
imi-bigpicture / opentile
Python library for reading tiles from wsi tiff-files.
digital-pathology tiff whole-slide-image
Language:Python 13