Topic: digital-pathology Goto Github

👇 Here are 88 public repositories matching this topic...

adalbertocq / learning-a-low-dimensional-manifold-of-realcancer-tissue
digital-pathology,Corresponding code of 'Quiros A.C., Murray-Smith R., Yuan K. Learning a low dimensional manifold of real cancer tissue with PathologyGAN 2020'.
User: adalbertocq
generative-adversarial-network histopathology representation-learning gans digital-pathology

adalbertocq / pathology-gan
digital-pathology,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'
User: adalbertocq
gans generative-adversarial-network representation-learning pathology-gan digital-pathology histopathology

aican-research / breast-epithelium-segmentation
digital-pathology,🌸 Breast epithelium segmentation through IHC-guided supervision
Organization: aican-research
breast-cancer deep-learning digital-pathology hematoxylin-eosin-staining immunohistochemistry fastpathology histopathology segmentation epithelium benign

aican-research / fast-pathology
digital-pathology,⚡ Open-source software for deep learning-based digital pathology
Organization: aican-research
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

aican-research / h2g-net
digital-pathology,🚀 H2G-Net: Segmentation of breast cancer region from whole slide images
Organization: aican-research
h2g-net cnn tensorflow-keras digital-pathology computational-pathology u-net agu-net mobilenetv2 breast-cancer clustering

ajinkya-kulkarni / pyhistology
digital-pathology,Python package that uses colorspace-based segmentation to analyze histopathology images.
User: ajinkya-kulkarni
Home Page: https://pyhistology.streamlit.app/
collagen digital-pathology histology-images segmentation image-processing image-segmentation python

alvarillo89 / glands-detection
digital-pathology,🧠 A deep learning algorithm based on convolutional neural networks to detect glandular cells in digitalized biopsies of the prostate. Performed as bachelor thesis for the degree in computer engineering.
User: alvarillo89
computer-vision convolutional-neural-networks deep-learning deep-neural-networks digital-image-processing digital-pathology keras-tensorflow neural-network opencv prostate-cancer whole-slide-imaging

andreped / fast-stain-normalization
digital-pathology,:star2: GPU-accelerated stain normalization command line tool
User: andreped
histopathology-images digital-pathology stain-normalization deep-learning cpp python computational-pathology fast torch tensorflow

andreped / nocodeseg
digital-pathology,🔬 Code-free deep segmentation for computational pathology
User: andreped
deep-learning u-net fastpathology deepmib qupath digital-pathology open-datasets open-annotations convolutional-neural-networks semantic-segmentation

aws-samples / sagemaker-distributed-training-digital-pathology-images
digital-pathology,Distributed training of digital pathology tissue slide images using SageMaker and Horovod.
Organization: aws-samples
sagemaker distributed-training digital-pathology horovod

bayer-group / pado
digital-pathology,PAthological Data Obsession - cloud native digital pathology datasets
Organization: bayer-group
python digital-pathology

bayer-group / paquo
digital-pathology,PAthological QUpath Obsession - QuPath and Python conversations
Organization: bayer-group
digital-pathology qupath python

bayer-group / tiffslide
digital-pathology,TiffSlide - cloud native openslide-python replacement based on tifffile
Organization: bayer-group
digital-pathology python

bioimageinformatics / gleason_grade
digital-pathology,Code for gleason grading a whole slide in 1 minute or less
User: bioimageinformatics
svs openslide-python tensorflow digital-pathology gleason-grade whole-slide-imaging

btcrabb / slideseg
digital-pathology,A Python module that produces image patches and annotation masks from whole slide images for deep learning in digital pathology.
User: btcrabb
digital-pathology semantic-segmentation whole-slide-imaging convolutional-neural-networks

bydmitry / he-erbb2
digital-pathology,Scientific Reports volume 11, Article number: 4037 (2021)
User: bydmitry
computer-vision deep-learning pytorch digital-pathology breast-cancer whole-slide-image her2 trastuzumab finher finprog

camicroscope / camicroscope
digital-pathology,Digital pathology image viewer with support for human/machine generated annotations and markups.
Organization: camicroscope
camicroscope digital-pathology slide-images whole-slide-imaging

cielal / torch-staintools
digital-pathology,Pytorch-adaptation of GPU-accelerated StainTool's stain normalization algorithms
User: cielal
Home Page: https://cielal.github.io/torch-staintools/
pytorch reinhard stain-normalization macenko staintools vahadane computational-pathology digital-pathology gpu-acceleration stain-augmentation pytorch-staintools stain-separation

cwlkr / torchvahadane
digital-pathology,Gpu accelerated vahadane stain normalization for Digital Pathology workflows.
User: cwlkr
deep-learning digital-pathology gpu-acceleration stain-normalization computational-pathology domain-adaptation domain-shift pathology pytorch stain-separation

cytomine / cytomine-core
digital-pathology,Cytomine-Core is the main web server implementing the Cytomine API
Organization: cytomine
Home Page: http://doc.cytomine.org
cytomine digital-pathology machine-learning whole-slide-imaging computational-pathology

dana-farber-aios / pathml
digital-pathology,Tools for computational pathology
Organization: dana-farber-aios
Home Page: https://pathml.org
machine-learning digital-pathology computational-pathology biomedical-image-processing pathology histopathology spatial-transcriptomics image-analysis microscopy fluorescence-microscopy-imaging

dazhangyu123 / acmil
digital-pathology,WSI classification
User: dazhangyu123
bracs camelyon16 computational-pathology digital-pathology multiple-instance-learning pathology-image whole-slide-image acmil weakly-supervised-learning histopathology

eidoslab / torchstain
digital-pathology,Stain normalization tools for histological analysis and computational pathology
Organization: eidoslab
pytorch histopathology stain-normalization computational-pathology medical-imaging python digital-pathology numpy tensorflow

histolab / histolab
digital-pathology,Library for Digital Pathology Image Processing
Organization: histolab
Home Page: http://histolab.readthedocs.io
digital-pathology-data digital-pathology bioinformatics biology wsi hacktoberfest data-science python science-research research pathology

icbcbicc / focuslitenn
digital-pathology,Official PyTorch and MATLAB implementations of our MICCAI 2020 paper "FocusLiteNN: High Efficiency Focus Quality Assessment for Digital Pathology"
User: icbcbicc
Home Page: http://ivc.uwaterloo.ca/code/FocusLiteNN/FocusLiteNN.html
convolutional-neural-network deep-learning deep-neural-networks digital-pathology image-processing image-quality-assessment medical-image-processing network-distillation pathological-images pytorch

imagingdatacommons / slim
digital-pathology,Interoperable web-based slide microscopy viewer and annotation tool
Organization: imagingdatacommons
Home Page: https://imagingdatacommons.github.io/slim/
dicomweb oidc react digital-pathology idc-viewers

imi-bigpicture / opentile
digital-pathology,Python library for reading tiles from wsi tiff-files.
Organization: imi-bigpicture
digital-pathology whole-slide-image tiff

imi-bigpicture / wsidicom
digital-pathology,Python package for reading DICOM WSI file sets.
Organization: imi-bigpicture
whole-slide-image digital-pathology annotations dicom

koriavinash1 / digitalhistopath
digital-pathology,
User: koriavinash1
histopathology digital-pathology whole-slide-imaging deep-learning uncertainty-quantification digestpath paip camelyon16 camelyon camelyon17

mkatw / gnn-fibrosis
digital-pathology,Liver fibrosis classification using graph convolutional networks.
User: mkatw
digital-pathology

objectivepathology / zif
digital-pathology,Zoomable Image Format
Organization: objectivepathology
Home Page: http://zif.photo
tiff bigtiff zif zoomify zoomable file-format digital-pathology

okunator / cellseg_gsontools
digital-pathology,Feature extraction from GEOJson nuclei and tissue segmentation maps
User: okunator
Home Page: https://github.com/okunator/cellseg_gsontools
digital-pathology feature-extraction morphological-analysis nuclei-segmentation spatial-data-analysis tissue-segmentation

okunator / cellseg_models.pytorch
digital-pathology,Encoder-Decoder Cell and Nuclei segmentation models
User: okunator
Home Page: https://github.com/okunator/cellseg_models.pytorch
accelerate ai cell-segmentation cellpose digital-pathology hovernet microscopy ml nuclei-segmentation omnipose panoptic-segmentation pytorch pytorch-lightning stardist timm tissue-segmentation

pathologydatascience / hips
digital-pathology,Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
Organization: pathologydatascience
biomarker-discovery biomedical-image-processing breast-cancer computational-pathology digital-pathology survival-prediction explainable-ai

pathologydatascience / mutils_panoptic
digital-pathology,Amgad M, Salgado R, Cooper LA. A panoptic segmentation approach for tumor-infiltrating lymphocyte assessment: development of the MuTILs model and PanopTILs dataset. medRxiv 2022.01.08.22268814.
Organization: pathologydatascience
Home Page: https://www.medrxiv.org/content/10.1101/2022.01.08.22268814v3
computational-pathology convolutional-neural-networks deep-learning digital-pathology explainable-ai tumor-infiltrating-lymphocytes tumor-segmentation breast-cancer

qupath / qupath
digital-pathology,QuPath - Bioimage analysis & digital pathology
Organization: qupath
Home Page: https://qupath.github.io
bioimage-informatics image-processing digital-pathology pathology machine-learning cell-segmentation whole-slide-imaging bioimage-analysis cell-analysis imagej

rapidsai / cucim
digital-pathology,cuCIM - RAPIDS GPU-accelerated image processing library
Organization: rapidsai
Home Page: https://docs.rapids.ai/api/cucim/stable/
image-processing computer-vision medical-imaging microscopy digital-pathology cuda gpu nvidia image-analysis image-data

rikiyay / style-transfer-for-digital-pathology
digital-pathology,Learning domain-agnostic visual representation for computational pathology using medically-irrelevant style transfer augmentation
User: rikiyay
Home Page: https://arxiv.org/abs/2102.01678
computer-vision representation-learning style-transfer computational-pathology digital-pathology data-augumentation deep-learning

sagizty / puzzletuning
digital-pathology,The official repo of PuzzleTuning: Explicitly Bridge Pathological and Natural Image with Puzzles (arXiv: 2311.06712)
User: sagizty
computer-vision digital-pathology pre-training ssl transformer

smistad / fast
digital-pathology,A framework for high-performance medical image processing, neural network inference and visualization
User: smistad
Home Page: https://fast.eriksmistad.no
opencl visualization parallel-computing medical-imaging gpu-computing deep-learning streaming ultrasound digital-pathology image-processing

smujiang / wsipenmarkingremoval
digital-pathology,Remove pen-marking annotations on whole slide images(WSIs) for data achiving.
User: smujiang
image-normalization deep-learning digital-pathology gan image-inpainting image-restoration

smujiang / wsitools
digital-pathology,Tools for whole slide image (WSI) processing. Especially for (pairwise) patch extraction, annotation parsing and data preparation for deep learning purposes.
User: smujiang
pathological image-processing wis patch extraction openslide digital-pathology

srinidhipy / iccv-cdpath2021-id-8
digital-pathology,Official code for "Improving Self-supervised Learning with Hardness-aware Dynamic Curriculum Learning: An Application to Digital Pathology", ICCV, 2021, CDpath Workshop (Oral).
User: srinidhipy
Home Page: https://openaccess.thecvf.com/content/ICCV2021W/CDPath/html/Srinidhi_Improving_Self-Supervised_Learning_With_Hardness-Aware_Dynamic_Curriculum_Learning_An_Application_ICCVW_2021_paper.html
self-supervised-learning curriculum-learning digital-pathology deep-learning

srinidhipy / ssl_cr_histo
digital-pathology,Official code for "Self-Supervised driven Consistency Training for Annotation Efficient Histopathology Image Analysis" Published in Medical Image Analysis (MedIA) Journal, Oct, 2021.
User: srinidhipy
Home Page: https://doi.org/10.1016/j.media.2021.102256
self-supervised-learning digital-pathology camelyon16 breastpathq teacher-student-training annotation-efficient semi-supervised-learning deep-learning histopathology

steven22tom / labelslide
digital-pathology,LabelSlide is a slide annotation tool and label object bounding boxes in virtual slides (generally used in pathology)
User: steven22tom
annotations deep-learning digital-pathology labeltool openseadragon openslide pathology pathology-image python3

talhaqaiser / computational-pathology-reading-list
digital-pathology,Reading list for Computational Pathology
User: talhaqaiser
computational-pathology digital-pathology deep-learning machine-learning

tissueimageanalytics / tiatoolbox
digital-pathology,Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
Organization: tissueimageanalytics
Home Page: https://warwick.ac.uk/tia
python computational-pathology whole-slide-imaging deep-learning digital-pathology histopathology image-analysis machine-learning tissue-analysis tissue-segmentation

tissuumaps / tissuumapscore
digital-pathology,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.
Organization: tissuumaps
Home Page: https://tissuumaps.github.io/
bioinformatics computational biology gene-expression gene-expression-profiles digital-pathology

zhaoxuanma / deeplearning-digital-pathology
digital-pathology,Full package for applying deep learning to virtual slides.
User: zhaoxuanma
deep-learning digital-pathology keras caffe openslide tensorflow

zhengyushan / adaptive_color_deconvolution
digital-pathology,adaptive color deconvolution for paper "Zheng et al., CMPB, 2019"
User: zhengyushan
Home Page: http://zhengyushan.github.io
digital-pathology stain-normalization stain-separation stain-standardization color-normalization histological-images histopathological-image