jlockhar/GLASS-AI

Machine learning tool for analysis of lung adenocarcinoma tumors

Language: MATLAB - Size: 159 MB - Last synced: about 5 hours ago - Pushed: about 13 hours ago - Stars: 4 - Forks: 2

paul-tourniaire/MS-CLAM

Source code associated to the article "MS-CLAM: Mixed supervision for the classification and localization of tumors in Whole Slide Images" published in Medical Image Analysis.

Language: Python - Size: 712 KB - Last synced: about 8 hours ago - Pushed: 7 days ago - Stars: 1 - Forks: 0

rapidsai/cucim

cuCIM - RAPIDS GPU-accelerated image processing library

Language: Jupyter Notebook - Size: 23.7 MB - Last synced: about 11 hours ago - Pushed: about 19 hours ago - Stars: 317 - Forks: 55

histolab/histolab

Library for Digital Pathology Image Processing

Language: Python - Size: 365 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 344 - Forks: 54

TissueImageAnalytics/tiatoolbox

Computational Pathology Toolbox developed by TIA Centre, University of Warwick.

Language: Python - Size: 441 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 331 - Forks: 71

mahmoodlab/UNI

Towards a general-purpose foundation model for computational pathology - Nature Medicine

Language: Jupyter Notebook - Size: 5.79 MB - Last synced: 5 days ago - Pushed: 3 months ago - Stars: 204 - Forks: 26

Bayer-Group/paquo

PAthological QUpath Obsession - QuPath and Python conversations

Language: Python - Size: 819 KB - Last synced: 5 days ago - Pushed: 10 days ago - Stars: 100 - Forks: 16

mahmoodlab/CLAM

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

Language: Python - Size: 45.8 MB - Last synced: 5 days ago - Pushed: about 1 month ago - Stars: 927 - Forks: 320

mahmoodlab/CONCH

A vision-language foundation model for computational pathology - Nature Medicine

Language: Python - Size: 1.2 MB - Last synced: 5 days ago - Pushed: 2 months ago - Stars: 163 - Forks: 11

camicroscope/caMicroscope

Digital pathology image viewer with support for human/machine generated annotations and markups.

Language: JavaScript - Size: 99.9 MB - Last synced: about 12 hours ago - Pushed: about 20 hours ago - Stars: 227 - Forks: 287

GeorgeBatch/dependency-mil

[ISBI 2024] Accurate Subtyping of Lung Cancers by Modelling Class Dependencies

Language: Jupyter Notebook - Size: 344 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 0

Dana-Farber-AIOS/pathml

Tools for computational pathology

Language: Python - Size: 218 MB - Last synced: 5 days ago - Pushed: 23 days ago - Stars: 369 - Forks: 81

sb-ml-py/SlideOrganizer

A simple python program to organize a digital slide collection as an SQLite database

Language: Python - Size: 11.3 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

CielAl/torch-staintools

Pytorch-adaptation of GPU-accelerated StainTool's stain normalization algorithms

Language: Python - Size: 73.9 MB - Last synced: 8 days ago - Pushed: 4 months ago - Stars: 15 - Forks: 3

ImagingDataCommons/slim

Interoperable web-based slide microscopy viewer and annotation tool

Language: TypeScript - Size: 71.2 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 110 - Forks: 36

smistad/FAST

A framework for high-performance medical image processing, neural network inference and visualization

Language: C++ - Size: 19.2 MB - Last synced: 12 days ago - Pushed: about 1 month ago - Stars: 415 - Forks: 98

AICAN-Research/FAST-Pathology

⚡ Open-source software for deep learning-based digital pathology

Language: C++ - Size: 81.1 MB - Last synced: 7 days ago - Pushed: 3 months ago - Stars: 116 - Forks: 23

EIDOSLAB/torchstain

Stain normalization tools for histological analysis and computational pathology

Language: Python - Size: 2.48 MB - Last synced: 22 days ago - Pushed: 2 months ago - Stars: 102 - Forks: 22

imi-bigpicture/wsidicom

Python package for reading DICOM WSI file sets.

Language: Python - Size: 1.08 MB - Last synced: 15 days ago - Pushed: 3 months ago - Stars: 30 - Forks: 6

okunator/cellseg_models.pytorch

Encoder-Decoder Cell and Nuclei segmentation models

Language: Python - Size: 68.2 MB - Last synced: 25 days ago - Pushed: 8 months ago - Stars: 63 - Forks: 3

smujiang/WSITools

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

Language: Python - Size: 5.72 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 30 - Forks: 11

andreped/NoCodeSeg

🔬 Code-free deep segmentation for computational pathology

Language: Jupyter Notebook - Size: 11.2 MB - Last synced: 22 days ago - Pushed: 7 months ago - Stars: 46 - Forks: 15

Bayer-Group/tiffslide

TiffSlide - cloud native openslide-python replacement based on tifffile

Language: Python - Size: 1.26 MB - Last synced: 25 days ago - Pushed: 4 months ago - Stars: 75 - Forks: 11

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'

Language: Python - Size: 547 MB - Last synced: 21 days ago - Pushed: almost 3 years ago - Stars: 90 - Forks: 20

imi-bigpicture/opentile

Python library for reading tiles from wsi tiff-files.

Language: Python - Size: 2.29 MB - Last synced: 21 days ago - Pushed: 4 months ago - Stars: 15 - Forks: 3

vggls/medical_xai

On the evaluation of deep learning interpretability methods for medical images under the scope of faithfulness

Language: Jupyter Notebook - Size: 47.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 0

mahmoodlab/CPATH_demographics

Demographic bias in misdiagnosis by computational pathology models - Nature Medicine

Language: Python - Size: 1.04 MB - Last synced: 5 days ago - Pushed: about 1 month ago - Stars: 12 - Forks: 2

georg-wolflein/hoechstgan

This repository contains official code for the WACV 2023 paper "HoechstGAN: Virtual Lymphocyte Staining Using Generative Adversarial Networks".

Language: Python - Size: 1.35 MB - Last synced: 29 days ago - Pushed: about 1 year ago - Stars: 4 - Forks: 0

MWod/DeeperHistReg

DeeperHistReg - Source Code

Language: Jupyter Notebook - Size: 11.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 3 - Forks: 0

open-pathology/awesome-pathology

Awesome List of Digital and Computational Pathology Resources

Size: 95.7 KB - Last synced: 20 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

mahmoodlab/MI-Zero

Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images - CVPR 2023

Language: Python - Size: 1.94 MB - Last synced: about 1 month ago - Pushed: 12 months ago - Stars: 78 - Forks: 3

AdalbertoCq/Learning-a-low-dimensional-manifold-of-realcancer-tissue

Corresponding code of 'Quiros A.C., Murray-Smith R., Yuan K. Learning a low dimensional manifold of real cancer tissue with PathologyGAN 2020'.

Language: Python - Size: 50.4 MB - Last synced: 21 days ago - Pushed: over 2 years ago - Stars: 7 - Forks: 1

Naveiras-Lab/MarrowQuant

MarrowQuant is a user-friendly algorithm for the quantification of H&E bone marrow tissue biopsies in whole slide images, implemented as a series of QuPath Scripts. Keywords: Digital Pathology, Whole slide Imaging, QuPath, Bone Marrow, Adiposity

Language: Groovy - Size: 28.5 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 5 - Forks: 1

sagizty/PuzzleTuning

The official repo of PuzzleTuning: Explicitly Bridge Pathological and Natural Image with Puzzles (arXiv: 2311.06712)

Language: Jupyter Notebook - Size: 39.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 6 - Forks: 0

dazhangyu123/ACMIL

WSI classification

Language: Python - Size: 4.64 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 21 - Forks: 2

qupath/qupath

QuPath - Bioimage analysis & digital pathology

Language: Java - Size: 93.5 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 962 - Forks: 267

mc2-center/nf-histoqc

A Nextflow wrapper for HistoQC

Language: Nextflow - Size: 1.75 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 1

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.

Language: Python - Size: 8.69 MB - Last synced: 5 days ago - Pushed: over 2 years ago - Stars: 62 - Forks: 21

ViacheslavDanilov/histology_segmentation

This repository is dedicated to the segmentation of histological features in regenerated vascular tissues obtained from tissue-engineered vascular grafts (TEVGs) implanted in sheep.

Language: Python - Size: 60 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

AICAN-Research/H2G-Net

🚀 H2G-Net: Segmentation of breast cancer region from whole slide images

Language: TeX - Size: 41.2 MB - Last synced: 22 days ago - Pushed: 5 months ago - Stars: 19 - Forks: 4

okunator/cellseg_gsontools

Feature extraction from GEOJson nuclei and tissue segmentation maps

Language: Python - Size: 82.2 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 8 - Forks: 0

SBU-BMI/wsinfer-mil

CLI tool to run specimen-level inference on whole slide images

Language: Python - Size: 39.1 KB - Last synced: 4 days ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

Bayer-Group/pado

PAthological Data Obsession - cloud native digital pathology datasets

Language: Python - Size: 888 KB - Last synced: 25 days ago - Pushed: over 1 year ago - Stars: 17 - Forks: 2

cwlkr/torchvahadane

Gpu accelerated vahadane stain normalization for Digital Pathology workflows.

Language: Python - Size: 80 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 4 - Forks: 2

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.

Language: JavaScript - Size: 14.4 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 20 - Forks: 2

fuminaba/Projects

Repository of my projects that I've done for fun or while exploring some topic in data science, machine/deep learning.

Language: Jupyter Notebook - Size: 50.8 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

AICAN-Research/breast-epithelium-segmentation

🌸 Breast epithelium segmentation through IHC-guided supervision

Language: Python - Size: 405 KB - Last synced: 22 days ago - Pushed: about 2 months ago - Stars: 9 - Forks: 3

dmandache/sleek-patch

Python 3 Package for optimally sampling big images with texture-aware patchification based on SLIC superpixels. So Sleek !

Language: Python - Size: 30.1 MB - Last synced: 3 months ago - Pushed: 5 months ago - Stars: 2 - Forks: 0

MohamedOmar2020/QuPath_scripts

Custom groovy scripts for QuaPath

Language: Groovy - Size: 8.79 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

RhDm/dogsled

Macenko normalisation of big medical slides

Language: Python - Size: 58.3 MB - Last synced: 21 days ago - Pushed: 7 months ago - Stars: 3 - Forks: 0

andreped/fast-stain-normalization

:star2: GPU-accelerated stain normalization command line tool

Language: Python - Size: 7.47 MB - Last synced: 22 days ago - Pushed: 8 months ago - Stars: 19 - Forks: 2

btcrabb/SlideSeg

A Python module that produces image patches and annotation masks from whole slide images for deep learning in digital pathology.

Language: Jupyter Notebook - Size: 101 KB - Last synced: 11 days ago - Pushed: almost 2 years ago - Stars: 78 - Forks: 26

andreped/FP-DSA-plugin

Digital Slide Archive plugin to enable FAST deployment of pretrained CNNs for digital pathology

Language: Python - Size: 6.77 MB - Last synced: 22 days ago - Pushed: 7 months ago - Stars: 5 - Forks: 1

cwalshai/beatson-augmentation-stain-normalisation-toolkit

Whole Slide Image Stain Normalisation and Augmentation

Language: Python - Size: 46.9 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

icbcbicc/FocusLiteNN

Official PyTorch and MATLAB implementations of our MICCAI 2020 paper "FocusLiteNN: High Efficiency Focus Quality Assessment for Digital Pathology"

Language: Python - Size: 4.75 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 35 - Forks: 5

radxtools/radpathfusion

Jupyter notebook with Python-based workflow for co-registration of radiographic imaging (MRI/CT etc.) with digitized pathology images, and mapping annotations from pathology onto imaging.

Language: Jupyter Notebook - Size: 99.3 MB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

dkurt/qupath-extension-openvino

Intel OpenVINO extension for QuPath, a digital pathology platform

Language: Java - Size: 89.8 KB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0

cytomine/Cytomine-core

Cytomine-Core is the main web server implementing the Cytomine API

Language: Groovy - Size: 245 MB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 69 - Forks: 27

bydmitry/he-erbb2

Scientific Reports volume 11, Article number: 4037 (2021)

Language: Python - Size: 3.1 MB - Last synced: 8 months ago - Pushed: over 3 years ago - Stars: 5 - Forks: 1

leosfan/fastq2dcc

Install the GeoMxNGSPipeline_Linux_2.0.0.16 tool from Nanostring/illumina to docker container, and convert it to Singularity.

Size: 3.91 KB - Last synced: 8 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

Bayer-Group/pavo

PAthological Visualization Obsession - visualization playground for pado datasets

Language: Python - Size: 1.2 MB - Last synced: 10 days ago - Pushed: 11 months ago - Stars: 5 - Forks: 2

MiriamAng/TilGenPro

Python-based pipeline for tiles generation and pre-processing from digitized histopathological images.

Language: Python - Size: 440 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 3

CirculatoryHealth/ExpressScan_Glycophorin

Scripts used for the "Glycophorin C in carotid atherosclerotic plaque reflects intraplaque hemorrhage and pre-procedural neurological symptoms" paper.

Language: HTML - Size: 4.01 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

PathologyDataScience/HiPS

Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis

Language: Python - Size: 35.2 KB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

ajinkya-kulkarni/PyHistology

Python package that uses colorspace-based segmentation to analyze histopathology images.

Language: Python - Size: 73.1 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 11 - Forks: 3

PathologyDataScience/MuTILs_Panoptic

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.

Language: Python - Size: 114 KB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 3 - Forks: 0

cornish/anonymize-slide-python3-gui

Delete the label image to deidentify a whole-slide image (WSI) with an optional GUI

Language: Python - Size: 33.2 KB - Last synced: 3 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 1

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).

Language: Python - Size: 1.19 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 14 - Forks: 6

compbio-ai/openslide-bundle

A python package bundling the openslide C and python libraries for automated path management

Language: JavaScript - Size: 23.3 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

ome/ecdp2019-publication

Supplementary information associated with Besson et al. (2019) ECDP 2019

Language: Python - Size: 6.43 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 3

aravi11/EAGNN

Official PyTorch Implementation of paper 'Edge-Based Graph Neural Networks for Cell-Graph Modeling and Prediction'

Language: Python - Size: 3.56 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

rikiyay/style-transfer-for-digital-pathology

Learning domain-agnostic visual representation for computational pathology using medically-irrelevant style transfer augmentation

Language: Python - Size: 107 MB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 20 - Forks: 7

pouyaka/tube_segmentation

tubular structure segmentation in histopathological images

Language: Python - Size: 188 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

elijahedmondson/QuPath-scripts

A collection of groovy scripts for digital pathology

Language: Groovy - Size: 101 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 4 - Forks: 1

sumanthratna/viewmask

A Python package and CLI to visualize segmentation masks.

Language: Python - Size: 9.77 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

mkatw/gnn-fibrosis

Liver fibrosis classification using graph convolutional networks.

Language: Python - Size: 28.3 KB - Last synced: over 1 year ago - Pushed: over 2 years ago - Stars: 8 - Forks: 1

smujiang/CellularComposition

Interactive modules to digitally annotate H&E whole slide images, construct cell and tissue level features and classify cell types. Specifically for a case study of differentiating borderline and high-grade serous ovarian tumors.

Language: Python - Size: 37.5 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 4 - Forks: 1

smujiang/WSIPenMarkingRemoval

Remove pen-marking annotations on whole slide images(WSIs) for data achiving.

Language: Python - Size: 13.8 MB - Last synced: over 1 year ago - Pushed: almost 2 years ago - Stars: 11 - Forks: 2

koriavinash1/DigitalHistoPath

Language: Jupyter Notebook - Size: 373 KB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 23 - Forks: 9

smujiang/TumorStromaReaction

Quantitatively evaluate tumor stroma reaction within ovarian cancers, and establish assocaitaions to prognosis, molecular signatures.

Language: Python - Size: 18.3 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

Zhengyushan/adaptive_color_deconvolution

adaptive color deconvolution for paper "Zheng et al., CMPB, 2019"

Language: Python - Size: 24.1 MB - Last synced: over 1 year ago - Pushed: over 3 years ago - Stars: 26 - Forks: 14

ccipd/DL-kidneyhistologicprimitives

Deep Learning for Kidney Histologic Primitives (U-Net implementation in PyTorch)

Language: Jupyter Notebook - Size: 745 MB - Last synced: over 1 year ago - Pushed: over 3 years ago - Stars: 3 - Forks: 4

alvarillo89/Glands-detection

🧠 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.

Language: Python - Size: 31 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 3 - Forks: 2

talhaqaiser/Computational-Pathology-Reading-List

Reading list for Computational Pathology

Size: 1.95 KB - Last synced: 10 months ago - Pushed: almost 6 years ago - Stars: 6 - Forks: 0

RobinHCK/Real-time-detection-for-renal-pathology Fork of qqwweee/keras-yolo3

A Keras implementation of YOLOv3 (Tensorflow backend)

Language: Python - Size: 3.01 MB - Last synced: over 1 year ago - Pushed: over 2 years ago - Stars: 3 - Forks: 1

Dana-Farber/self-supervised-learning-review-in-medicine

Self-Supervised Learning in Medicine Review

Size: 331 KB - Last synced: 11 months ago - Pushed: almost 2 years ago - Stars: 5 - Forks: 0

aws-samples/sagemaker-distributed-training-digital-pathology-images

Distributed training of digital pathology tissue slide images using SageMaker and Horovod.

Language: Jupyter Notebook - Size: 279 KB - Last synced: over 1 year ago - Pushed: about 3 years ago - Stars: 7 - Forks: 4

Digital-Pathology/ML-Supervised

Language: Python - Size: 145 KB - Last synced: over 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

afiliot/TPDUIA

DU Intelligence Artificielle et Santé (CHU de Lille). Séminaire 4: Traitement de l'image.

Language: Jupyter Notebook - Size: 102 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

PathologyDataScience/MatDigitalPathology

Matlab functions to support analysis of digital pathology images.

Language: Matlab - Size: 24.4 KB - Last synced: over 1 year ago - Pushed: over 7 years ago - Stars: 3 - Forks: 3

BioImageInformatics/gleason_grade

Code for gleason grading a whole slide in 1 minute or less

Language: Jupyter Notebook - Size: 28.6 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 5 - Forks: 5

BioImageInformatics/svs_reader

Convenient interface for generating tiles from Aperio SVS format images

Language: Python - Size: 55.7 KB - Last synced: over 1 year ago - Pushed: about 5 years ago - Stars: 2 - Forks: 1