adnaanz/lsu

Compute LSU factorization of a matrix in PyTorch

Language: Python - Size: 19.5 KB - Last synced at: about 11 hours ago - Pushed at: about 12 hours ago - Stars: 0 - Forks: 0

TissueImageAnalytics/tiatoolbox

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

Language: Python - Size: 505 MB - Last synced at: about 13 hours ago - Pushed at: about 13 hours ago - Stars: 426 - Forks: 89

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.

Language: Java - Size: 267 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 397 - Forks: 250

qupath/qupath

QuPath - Open-source bioimage analysis for research

Language: Java - Size: 96.2 MB - Last synced at: 2 days ago - Pushed at: 5 days ago - Stars: 1,152 - Forks: 299

mahmoodlab/CLAM

Open source tools for computational pathology - Nature BME

Language: Python - Size: 45.8 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 1,317 - Forks: 419

AImageLab-zip/MONKEY_challenge_ziplab

AImageLab Zip UNIMORE solution for the MONKEY Challenge of Radboud University Medical Center

Language: Jupyter Notebook - Size: 336 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 0

cylab-tw/bluelight

a browser-based DICOM viewer

Language: JavaScript - Size: 8.28 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 133 - Forks: 47

cgohlke/tifffile

Read and write TIFF files.

Language: Python - Size: 2.16 MB - Last synced at: 3 days ago - Pushed at: 6 days ago - Stars: 595 - Forks: 160

lucasrla/wsi-preprocessing

Simple library for preprocessing histopathological whole-slide images (WSI) into tiles (a.k.a. patches) towards deep learning

Language: Python - Size: 18.6 KB - Last synced at: 4 days ago - Pushed at: over 1 year ago - Stars: 53 - Forks: 14

lucasrla/wsi-tile-cleanup

Image filters for digital pathology: detect pen marks, background, and artifacts. Use them for preprocessing towards deep learning

Language: Python - Size: 3.6 MB - Last synced at: 4 days ago - Pushed at: over 4 years ago - Stars: 28 - Forks: 4

DeepMicroscopy/Exact

An open source online platform for collaborative image labeling of almost everything

Language: JavaScript - Size: 118 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 59 - Forks: 19

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]

Language: Python - Size: 94.3 MB - Last synced at: 10 days ago - Pushed at: 18 days ago - Stars: 193 - Forks: 76

computationalpathologygroup/ASAP

Program for the analysis and visualization of whole-slide images in digital pathology

Language: C++ - Size: 7 MB - Last synced at: 10 days ago - Pushed at: over 1 year ago - Stars: 640 - Forks: 168

MarvinLer/tcga_segmentation

Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024

Language: Python - Size: 63.1 MB - Last synced at: 10 days ago - Pushed at: almost 4 years ago - Stars: 134 - Forks: 34

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.

Language: Python - Size: 93.7 MB - Last synced at: 10 days ago - Pushed at: 6 months ago - Stars: 100 - Forks: 30

openslide/openslide

C library for reading virtual slide images

Language: C - Size: 4.22 MB - Last synced at: 3 days ago - Pushed at: 20 days ago - Stars: 431 - Forks: 227

open-pathology/awesome-pathology

Awesome List of Digital and Computational Pathology Resources

Size: 174 KB - Last synced at: 10 days ago - Pushed at: 4 months ago - Stars: 52 - Forks: 3

slideflow/slideflow

Powerful, open-source AI tools for digital pathology.

Language: Python - Size: 133 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 298 - Forks: 50

julimer228/EPIIC

Edge-Preserving Method Increasing nucleI Clarity for Compression Artifacts Removal in Whole-Slide Histopathological Images

Language: MATLAB - Size: 14.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

baidu-research/NCRF

Cancer metastasis detection with neural conditional random field (NCRF)

Language: Python - Size: 97.1 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 764 - Forks: 184

SBU-BMI/wsinfer

🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images

Language: Python - Size: 2.05 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 69 - Forks: 12

sara-nl/2D-VQ-AE-2

2D Vector-Quantized Auto-Encoder for compression of Whole-Slide Images in Histopathology

Language: Python - Size: 39 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 16 - Forks: 2

cpathology/NucleiSegHE

H&E ROI-Level and WSI-Level Nuclei Segmentation with HoVer-Net

Language: Python - Size: 10.4 MB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 9 - Forks: 3

camicroscope/caMicroscope

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

Language: JavaScript - Size: 100 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 269 - Forks: 312

SBU-BMI/SpinPath

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

Language: Python - Size: 44.9 KB - Last synced at: 1 day ago - Pushed at: 4 months ago - Stars: 5 - Forks: 0

WonderLandxD/opensdpc

Python library for processing whole slide images (WSIs) in sdpc format

Language: Jupyter Notebook - Size: 62.4 MB - Last synced at: 20 days ago - Pushed at: 4 months ago - Stars: 51 - Forks: 10

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 at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 78 - Forks: 24

MIDA-group/CytoBrowser

CytoBrowser, a JavaScript and Node.js driven environment for fast and accessible collaborative online visualization, assessment, and annotation of very large microscopy images.

Language: JavaScript - Size: 4.77 MB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 18 - Forks: 8

luisvalesilva/wsipre

Handling whole-slide images with region-level annotations.

Language: Jupyter Notebook - Size: 7.55 MB - Last synced at: 27 days ago - Pushed at: over 6 years ago - Stars: 10 - Forks: 5

mahmoodlab/CRANE

Deep learning enabled assessment of cardiac allograft rejection from endomyocardial biopsies- Nature Medicine

Language: Python - Size: 4.16 MB - Last synced at: 18 days ago - Pushed at: almost 3 years ago - Stars: 31 - Forks: 8

jgamper/compay-syntax

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

Language: Python - Size: 43.5 MB - Last synced at: 10 days ago - Pushed at: over 2 years ago - Stars: 55 - Forks: 1

episphere/imagebox3

Tile Serving on the web without a server

Language: JavaScript - Size: 456 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 12 - Forks: 1

GoogleCloudPlatform/qupath-chcapi-extension 📦

Extension to QuPath application adding support for reading from Google Cloud Healthcare API.

Language: Java - Size: 16.1 MB - Last synced at: 27 days ago - Pushed at: over 3 years ago - Stars: 22 - Forks: 11

BiologyTools/BioImager

A .NET microscopy imaging application based on Bio library. Supports various microscopes by using imported libraries & GUI automation. Supports XInput game controllers to move stage, take images, run ImageJ macros on images or Bio C# scripts.

Language: C# - Size: 73.5 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 17 - Forks: 5

Mmasoud1/HistoJS

HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

Language: JavaScript - Size: 290 MB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 19 - Forks: 0

clementapa/Prostate-Cancer-Image-Classification

Deep Learning for medical imaging kaggle challenge for the MVA master 2021-2022. Classification of ISUP grades from Whole Slide Images.

Language: Jupyter Notebook - Size: 25 MB - Last synced at: 10 days ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 2

liupei101/Pipeline-Processing-TCGA-Slides-for-MIL

This repo provides the pipeline of processing TCGA whole-slide images for downstream pathology analysis.

Language: Python - Size: 14.8 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 55 - Forks: 11

koriavinash1/DigitalHistoPath

Language: Jupyter Notebook - Size: 373 KB - Last synced at: 11 days ago - Pushed at: over 2 years ago - Stars: 24 - Forks: 8

ChongQingNoSubway/DGR-MIL

Code for paper: DGR-MIL: Exploring Diverse Global Representation in Multiple Instance Learning for Whole Slide Image Classification [ECCV 2024]

Language: Python - Size: 2.29 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 128 - Forks: 4

cpystan/WSI-VQA

[ECCV 2024] Official Implementation of 《WSI-VQA: Interpreting Whole Slide Image by Generative Question Answering》

Language: Python - Size: 25.2 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 30 - Forks: 1

ImagingDataCommons/dicomslide

Python library for reading whole slide images in DICOM format

Language: Python - Size: 173 KB - Last synced at: 4 days ago - Pushed at: about 1 year ago - Stars: 9 - Forks: 3

patolojiatlasi/patolojiatlasi.github.io

Patoloji Atlası

Language: HTML - Size: 745 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 9 - Forks: 1

patolojiatlasi/EN

Pathology Atlas (English version of Patoloji Atlası)

Language: HTML - Size: 378 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

jamesdolezal/biscuit

Bayesian Inference of Slide-level Confidence via Uncertainty Index Thresholding

Language: Python - Size: 599 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 26 - Forks: 2

Naxocist/AILCAP

An implementation of deep learning segmentation models in digital pathology field

Language: JavaScript - Size: 373 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

UESTC-nnLab/ProDiv

[CMPB 2024] ProDiv: Prototype-driven consistent pseudo-bag division for whole-slide image classification

Language: Python - Size: 995 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 5 - Forks: 0

kaczmarj/geojson2tif

Convert GeoJSON of polygons to pyramical TIF images

Language: Python - Size: 2.36 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1

ChongQingNoSubway/PDL

Code for the paper " PDL: Regularizing Multiple Instance Learning with Progressive Dropout Layers "

Language: Python - Size: 1.44 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 113 - Forks: 29

peterlipan/Awesome-Multi-instance-Learning-for-Whole-Slide-Images

A curated list of awesome Multi-instance Learning frameworks for Whole Slide Images (WSIs) classification, segmentation, etc.

Size: 4.88 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

MiriamAng/TilGenPro

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

Language: Python - Size: 440 KB - Last synced at: 11 months ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 3

SamaNematy/WSI-Shading-Correction Fork of pair-kopti/Shading-correction

Implementation of state of the art algorithms for uneven illomination correction in whole slide imaging

Language: Jupyter Notebook - Size: 7.03 GB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

MihirBafna/metaDetect

Platform for identifying metaphase spreads in a population of cells from whole slide images using Computer Vision techniques

Language: Python - Size: 22.5 MB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

liupei101/DSCA

[ESWA 2023] Implementation of DSCA: A Dual-stream Network with Cross-attention on Whole-Slide Image Pyramids for Cancer Prognosis

Language: Python - Size: 6.21 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 19 - Forks: 5

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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 1

AshkanShakarami/TCNN

TCNN: A Transformer Convolutional Neural Network for artifact classification in whole slide images

Language: Jupyter Notebook - Size: 4.78 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

binli123/dsmil-wsi

DSMIL: Dual-stream multiple instance learning networks for tumor detection in Whole Slide Image

Language: Python - Size: 48.1 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 302 - Forks: 82

yujota/elm-asap-pathology-format

Elm library providing encoder/decoder for automated slide analysis platform XML format (https://github.com/computationalpathologygroup/ASAP).

Language: Elm - Size: 32.2 KB - Last synced at: 2 months ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 1

PingjunChen/tissueloc

Whole Slide Digital Pathology Image Tissue Localization

Language: Python - Size: 22.2 MB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 44 - Forks: 12

PingjunChen/pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

Language: Python - Size: 18.6 MB - Last synced at: 10 days ago - Pushed at: about 2 years ago - Stars: 48 - Forks: 8

namandangi/wsi

Image Processing and CV on Whole Slide Images

Language: Jupyter Notebook - Size: 8.82 MB - Last synced at: 14 days ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 1

liupei101/GraphLSurv

GraphLSurv: A Scalable Survival Prediction Network with Adaptive and Sparse Structure Learning for Histopathological Whole-Slide Images

Language: Jupyter Notebook - Size: 16.8 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 2

rashindrie/ANSAC

Classification of whole-slide images based on tumor infiltrating lymphocyte grades using image-level labels

Language: Python - Size: 354 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

c-arthurs/QuArray

An application for exporting and analysing tissue array whole slide image files

Language: Python - Size: 22.7 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 7 - Forks: 3

YashSharma/C2C

Implementation of Cluster-to-Conquer: A Framework for End-to-End Multi-Instance Learning for Whole Slide Image Classification approach.

Language: Python - Size: 2.27 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 51 - Forks: 12

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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

tand826/wsiprocess

Whole Slide Image (WSI) Processing Library for Histopathological / Cytopathological Machine Learning Tasks

Language: Python - Size: 10.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 3

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 at: about 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1

cpathology/Pyramidal-TIFF

Convert Slides/Images to Pyramidal TIFF Format

Language: Python - Size: 23.4 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 2

ysbecca/fwat

A Fast Whole-slide image Annotation Tool (FWAT) for conducting painless studies requiring annotations on whole-slide images.

Language: JavaScript - Size: 3.45 MB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 10 - Forks: 1

lucasrla/wsi-preprocessing-sos-workflow

A pipeline to preprocess whole-slide images (WSI) towards deep learning

Size: 14.6 KB - Last synced at: 4 days ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 2

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 at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

IDR/idr0042-nirschl-wsideeplearning

Metadata files for the idr0042 submission

Language: Python - Size: 212 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 6

ome/ecdp2019-publication

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

Language: Python - Size: 6.43 MB - Last synced at: 7 days ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 3

CirculatoryHealth/EntropyMasker

A fully automated approach for separating foreground (tissue) and background in bright-field microscopic whole-slide images of (immuno)histologically stained samples.

Language: Jupyter Notebook - Size: 8.06 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

aaqdas/wsi-scanner-segmentation

Whole Slide Image Segmentation

Language: Jupyter Notebook - Size: 40.6 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

c-arthurs/labelstrip

GUI wrapped around anonymise label for SVS and NDPI whole slide images

Language: Python - Size: 915 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 8 - Forks: 2

uw-loci/demo_wsi_superres

WSISR: Single image super-resolution for Whole slide Imaging using convolutional neural networks and self-supervised color normalization.

Language: Python - Size: 9.61 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 15 - Forks: 4

uzunb/deep-zoom-image-viewer

This is a viewer app that provides using to zoom and pan tools Deep Zoom Image (dzi) or Whole Slide Image (wsi) using Electron JS and OpenSeaDragon .

Language: JavaScript - Size: 32.8 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 1

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 at: about 2 years ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 2

YashSharma/HistoTransfer

Implementation of HistoTransfer published in IEEE-BHI 2021.

Language: Jupyter Notebook - Size: 8.56 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 3

sacmehta/WSISegmentation

Segmenting WSIs using Deep Convolutional Neural Networks

Language: Lua - Size: 3.06 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 16 - 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 at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 5

cshukai/tcga_colorectal_histology_images

Language: Python - Size: 122 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1