GitHub topics: whole-slide-image
mahmoodlab/TRIDENT
Toolkit for large-scale whole-slide image processing.
Language: Python - Size: 3.09 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 348 - Forks: 63
imi-bigpicture/wsidicom
Python package for reading DICOM WSI file sets.
Language: Python - Size: 1.9 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 44 - Forks: 9
rmuraix/HistoSlice
Preprocessing module for large histological images
Language: Python - Size: 27.9 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0
okunator/cellseg_gsontools
Feature extraction from GEOJson nuclei and tissue segmentation maps
Language: Python - Size: 88.1 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 15 - Forks: 0
AICAN-Research/H2G-Net
🚀 H2G-Net: Segmentation of breast cancer region from whole slide images
Language: Jupyter Notebook - Size: 61.8 MB - Last synced at: 7 days ago - Pushed at: about 2 months ago - Stars: 28 - Forks: 8
Franblueee/torchmil
Deep Multiple Instance Learning library for Pytorch
Language: Python - Size: 7.72 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 50 - Forks: 2
mahmoodlab/MIL-Lab
Feather - Lightweight supervised slide foundation models (ICML 2025)
Language: Python - Size: 396 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 67 - Forks: 3
histopathologyatlas/histopathologyatlas.github.io
Histopathology Atlas contains whole slide images of various diseases
Language: HTML - Size: 224 MB - Last synced at: 2 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
andreped/wsi-visualization-demo
🔬 Simple containerised whole slide image rendering in the browser
Language: HTML - Size: 16.9 MB - Last synced at: 7 days ago - Pushed at: 11 months ago - Stars: 3 - Forks: 0
BiologyTools/BioCore
Bio Library in .NET8. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.
Language: C# - Size: 107 MB - Last synced at: 15 days ago - Pushed at: 2 months ago - Stars: 4 - Forks: 1
BiologyTools/BioGTK
A cross platform version of Bio library & program. Bio is a library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.
Language: C# - Size: 146 MB - Last synced at: 2 days ago - Pushed at: 3 months ago - Stars: 14 - Forks: 2
lingxitong/MIL_BASELINE
A library that integrates different MIL methods into a unified framework
Language: Python - Size: 75.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 198 - Forks: 12
BiologyTools/Bio
A .NET library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.
Language: C# - Size: 28.9 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 0
agentdr1/LA_MIL
Implementation of LA_MIL, Local Attention Graph-based Transformer for WSIs, PyTorch
Language: Python - Size: 686 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 24 - Forks: 0
AICAN-Research/DRU-Net
🫁 DRU-Net: Lung carcinoma Segmentation using multi-lens distortion and fusion refinement network
Language: Python - Size: 120 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 1
huangzhii/nuclei.io
nuclei.io: Human-in-the-loop active learning framework for pathology image analysis
Language: Python - Size: 71.6 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 67 - Forks: 12
imi-bigpicture/opentile
Python library for reading tiles from wsi tiff-files.
Language: Python - Size: 2.46 MB - Last synced at: 20 days ago - Pushed at: 4 months ago - Stars: 16 - Forks: 4
dazhangyu123/ACMIL
Attention-Challenging Multiple Instance Learning for Whole Slide Image Classification (ECCV2024)
Language: Python - Size: 67.5 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 90 - Forks: 11
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: 4 months ago - Pushed at: 10 months ago - Stars: 100 - Forks: 30
dazhangyu123/AEM
AEM: Attention Entropy Maximization for Multiple Instance Learning based Whole Slide Image Classification
Language: Python - Size: 4.65 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 11 - Forks: 1
tueimage/MAD-MIL
Multi-head Attention-based Deep Multiple Instance Learning
Language: Python - Size: 69.9 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 4 - Forks: 1
tueimage/MIL-Reliability
Quantitative Evaluation of Multiple Instance Learning Reliability For WSIs Classification
Size: 13.7 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
titizheng/PAMIL
Implementation of "Dynamic Policy-Driven Adaptive Multi-Instance Learning for Whole Slide Image Classification", (CVPR 2024 Highlight).
Language: Python - Size: 31.2 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 14 - Forks: 0
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: 12 days ago - Pushed at: almost 3 years ago - Stars: 55 - Forks: 1
AmayaGS/MUSTANG
Multi-stain graph self attention multiple instance learning for histopathology Whole Slide Images - BMVC 2023
Language: Python - Size: 2.59 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 13 - Forks: 2
andreped/wsi-annotation-demo
🔬 Annotating whole slide images through the browser
Language: JavaScript - Size: 51.8 KB - Last synced at: 7 days ago - Pushed at: 11 months ago - Stars: 3 - Forks: 1
huuquan1994/wsi_glomerulus_seg
Glomerulus segmentation pipeline for Patch-level and WSI-level segmentation tasks
Size: 10.7 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
titizheng/SMILE
Code for paper "SMILE: Self-Motivated Multi-instance Learning for Whole Slide Image Classification" submission under review.
Language: Python - Size: 396 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 3 - Forks: 0
HKU-MedAI/HIGT
[MICCAI'23] HIGT: Hierarchical Interaction Graph-Transformer for Whole Slide Image Analysis
Language: Python - Size: 460 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 26 - 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: about 1 year ago - Pushed at: about 1 year ago - Stars: 113 - Forks: 29
StonyBrookDB/igt-wsi
Repository for "Integrative Graph-Transformer Framework for Histopathology Whole Slide Image Representation and Classification""
Size: 13.7 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
miccaiif/INS
Official Pytorch Code of Our Paper: Rethinking Multiple Instance Learning for Whole Slide Image Classification: A Good Instance Classifier is All You Need
Language: Python - Size: 2 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
miccaiif/DGMIL
Official PyTorch implementation of our MICCAI 2022 paper: DGMIL: Distribution Guided Multiple Instance Learning for Whole Slide Image Classification.
Language: Python - Size: 2.42 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 28 - Forks: 4
miccaiif/WENO
Official PyTorch implementation of our NeurIPS 2022 paper: Weakly Supervised Knowledge Distillation for Whole Slide Image Classification
Language: Python - Size: 1.59 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 52 - Forks: 12
liupei101/AdvMIL
[MedIA 2024] The implementation of AdvMIL: Adversarial Multiple Instance Learning for the Survival Analysis on Whole-Slide Images
Language: Python - Size: 2.18 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 21 - Forks: 8
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: over 1 year ago - Pushed at: over 1 year ago - Stars: 302 - Forks: 82
nadiabrancati/ABNN-WSI-Classification
Code to reproduce results of the Gigapixel Histopathological Image Analysis Using Attention-Based Neural Networks paper.
Language: Python - Size: 1.22 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 1
RhDm/dogsled
Macenko normalisation of big medical slides
Language: Python - Size: 58.3 MB - Last synced at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0
smujiang/Re-stained_WSIs_Registration
Re-stained whole slide image alignment
Language: Python - Size: 10.3 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 27 - Forks: 11
bydmitry/he-erbb2
Scientific Reports volume 11, Article number: 4037 (2021)
Language: Python - Size: 3.1 MB - Last synced at: 25 days ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 1
sauravmishra1710/Malaria-Detection-Using-Deep-Learning-Techniques
Malaria Parasite Detection using Efficient Neural Ensembles. Malaria, a life threatening disease caused by the bite of the Anopheles mosquito infected with the parasite, has been a major burden towards healthcare for years leading to approximately 400,000 deaths globally every year. This study aims to build an efficient system by applying ensemble techniques based on deep learning to automate the detection of the parasite using whole slide images of thin blood smears.
Language: Jupyter Notebook - Size: 295 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 5
daangeijs/simple_wsi_viewer
A simple web application for for viewing and navigating pathology whole-slide-images in your browser.
Language: JavaScript - Size: 9.57 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 7 - Forks: 1
fhnaumann/pathology-image-server
A pathology image server using DICOM and FHIR to manage WSI files.
Language: Java - Size: 1.29 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
nihaomiao/PRICAI18_MVF-CasCNN
The implementation of our pricai18 paper "Multiple Visual Fields Cascaded Convolutional Neural Network for Breast Cancer Detection."
Language: Python - Size: 555 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 6 - Forks: 3
nihaomiao/MLMI19_WSI-Net
The implementation of our MLMI19 oral paper "WSI-Net: Branch-based and Hierarchy-aware Network for Segmentation and Classification of Breast Histopathological Whole-slide Images."
Language: Python - Size: 241 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 6 - Forks: 0
Zhengyushan/kat
The code for Kernel attention transformer (KAT)
Language: Python - Size: 278 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 19 - Forks: 1
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: over 2 years ago - Pushed at: over 3 years ago - Stars: 15 - Forks: 4
Chrisa142857/You-Only-Look-Cytopathology-Once
Codes available of a paper: An Efficient Cervical Whole Slide Image Analysis Framework Based on Multi-scale Semantic and Location Deep Features.
Language: Python - Size: 25.7 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 13 - Forks: 5
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: over 2 years ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1
Atishaysjain/WSI-Nuclear-Segmentation
Performs instance segmentation and classification of nuclei in Multi-Tissue Histology WSIs(generally 100k*100k pixels).
Language: Jupyter Notebook - Size: 137 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 1
Zhengyushan/lagenet
The code for LAGE-Net
Language: Python - Size: 38.1 KB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 8 - Forks: 2
Zhengyushan/dpathnet
Code for the DRA-Net
Language: Python - Size: 61.5 KB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 1
NMPoole/CS5199-Dissertation
Dissertation completed for the award of MSci in Computer Science. This dissertation is about automated breast cancer detection in low-resolution whole-slide pathology images using a deep convolutional neural network pipeline.
Language: Python - Size: 16.8 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0
gatsby2016/Fast-WSI-Prediction
Unofficial implementation for ScanNet (a fast WSI prediction method) in PyTorch.
Language: Python - Size: 20.2 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 20 - Forks: 1
gatsby2016/DLforWSI
An effective deep learning classification framework for whole slide images.
Language: Python - Size: 1.91 MB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0