GitHub topics: wsi
sigma10010/med_img_seg
Scale-adaptive viable tumor burden estimation via histopathological microscopy image segmentation
Language: Jupyter Notebook - Size: 8.38 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 6 - Forks: 0
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: 4 days ago - Pushed at: 7 days ago - Stars: 397 - Forks: 251
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: 7 days ago - Pushed at: 7 days ago - Stars: 19 - Forks: 8
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: 8 days ago - Pushed at: 8 days ago - Stars: 2 - Forks: 1
histolab/histolab
Library for Digital Pathology Image Processing
Language: Python - Size: 365 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 409 - Forks: 62
cylab-tw/bluelight
a browser-based DICOM viewer
Language: JavaScript - Size: 8.22 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 134 - Forks: 48
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: 6 days ago - Pushed at: over 1 year ago - Stars: 54 - Forks: 14
computational-cell-analytics/patho-sam
Segment Anything for Histopathology
Language: Python - Size: 265 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 27 - Forks: 3
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: 6 days ago - Pushed at: over 4 years ago - Stars: 28 - Forks: 4
andreped/vsi2tif
Simple tool for converting WSIs from cellSens VSI to pyramidal TIFF
Language: Jupyter Notebook - Size: 604 KB - Last synced at: 1 day ago - Pushed at: 4 months ago - Stars: 20 - Forks: 6
mahmoodlab/Patch-GCN
Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks - MICCAI 2021
Language: Python - Size: 1.16 GB - Last synced at: 23 days ago - Pushed at: about 1 year ago - Stars: 148 - Forks: 28
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: 23 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: 23 days ago - Pushed at: 6 months ago - Stars: 100 - Forks: 30
Kitware/BANFF-AID
BANFF-AID: Banff Automated Nephrology Feature Framework - Artificial Intelligence Diagnosis
Language: Python - Size: 48.8 KB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 2 - Forks: 0
HaoyuCui/PyPathomics
PyPathomics is an open-source software for gigapixel whole-slide image analysis. Extract features directly from HoverNet's json file.
Language: Python - Size: 243 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 0
haranrk/DigiPathAI
Tool to visualize gigantic pathology images and use AI to segment cancer cells and present as an overlay
Language: JavaScript - Size: 138 MB - Last synced at: 5 days ago - Pushed at: 5 months ago - Stars: 72 - Forks: 27
manuel-munoz-aguirre/PyHIST
A pipeline to segment tissue from the background in histological images
Language: Python - Size: 55.2 MB - Last synced at: 23 days ago - Pushed at: about 2 years ago - Stars: 69 - Forks: 13
BMIRDS/deepslide
Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
Language: Python - Size: 11.2 MB - Last synced at: 22 days ago - Pushed at: 12 months ago - Stars: 504 - Forks: 141
aimagelab/mil4wsi
DAS-MIL: Distilling Across Scales for MILClassification of Histological WSIs
Language: Python - Size: 835 KB - Last synced at: about 2 months ago - Pushed at: 6 months ago - Stars: 56 - Forks: 6
LUMCPathAI/TCGA-Tools
Easy download and annotation extraction from public TCGA WSI datasets
Language: Python - Size: 10.1 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0
uit-hdl/feature-inspect
tools for UMAP and linear probe inspection
Language: Python - Size: 82 KB - Last synced at: about 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
titizheng/GraphMamba
Implementation of "GraphMamba: Whole Slide Image Classification Meets Graph-driven Selective State Space Model".
Language: Python - Size: 0 Bytes - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
cpystan/Wsi-Caption
Official Inplementation of 《WsiCaption: Multiple Instance Generation of Pathology Reports for Gigapixel Whole Slide Images》(MICCAI 2024 Oral/ Best Paper Candidate)
Language: Python - Size: 1.42 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 49 - Forks: 3
GoogleCloudPlatform/dicomweb-wsi-viewer 📦
Proof of concept whole slide imaging viewer on top of Google Cloud Healthcare DICOM API.
Language: JavaScript - Size: 17.6 KB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 40 - Forks: 15
xubiker/psimage
Python package to work with images in psi format
Size: 37.7 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 1
GoogleCloudPlatform/wsi-to-dicom-converter
Conversion tool/library for converting whole slide images to DICOM
Language: C++ - Size: 7.92 MB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 82 - Forks: 27
andreped/pathology-representation-simulation
🚀 Create your own simulation of t-SNE on histopathology images!
Language: Jupyter Notebook - Size: 17.3 MB - Last synced at: 1 day ago - Pushed at: 7 months ago - Stars: 4 - Forks: 0
andreped/wsi-annotation-demo
🔬 Annotating whole slide images through the browser
Language: JavaScript - Size: 51.8 KB - Last synced at: 1 day ago - Pushed at: 7 months ago - Stars: 3 - Forks: 0
KPMP/wsi-worker
A containerized worker to convert WSI slides in SVS format to DZI
Language: Python - Size: 121 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 1
histopathologyatlas/histopathologyatlas.github.io
Histopathology Atlas contains whole slide images of various diseases
Language: HTML - Size: 227 MB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0
xgwang1119/Wireless_Standard_Identification_WSI
To generate the waveform demo, for paper "Wireless Standard Identification via Mel Frequency Cepstrum" in IEEE Communications Letters, vol. 26, no. 11, pp. 2656-2660, Nov. 2022
Language: MATLAB - Size: 69.3 KB - Last synced at: 6 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
andreped/wsi-visualization-demo
🔬 Simple containerised whole slide image rendering in the browser
Language: HTML - Size: 16.9 MB - Last synced at: 1 day ago - Pushed at: 7 months ago - Stars: 2 - 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
cechlauren/DeeeepLearning
Repository of code for deep learning approaches on WSIs, IHC, H&E, etc.
Language: Groovy - Size: 1.16 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
KPMP/cassiopeia-data
Service layer for the participant whole slide image viewer
Language: Java - Size: 175 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0
KPMP/cassiopeia-web
Repo to store the front-end code for the Participant Whole Slide Image Viewer
Language: JavaScript - Size: 7.83 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 2 - Forks: 0
yjg30737/pyqt-wsi-viewer
PyQt WSI(Whole Slide Images) viewer
Language: Roff - Size: 19.3 MB - Last synced at: 9 days ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
Katalip/ca-stinv-cnn
Code for "Improving Stain Invariance of CNNs for Segmentation by Fusing Channel Attention and Domain-Adversarial Training"
Language: Python - Size: 16.8 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 0
DSLituiev/slideslicer
a toolbox for manipulation of digital pathology slides and annotations
Language: Jupyter Notebook - Size: 7.32 MB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 19 - Forks: 4
Jonas1312/PFA-ScanNet
PFA-ScanNet: Pyramidal Feature Aggregation With Synergistic Learning for Breast Cancer Metastasis Analysis (Architecture Only Pytorch Implementation).
Language: Python - Size: 505 KB - Last synced at: 1 day ago - Pushed at: almost 6 years ago - Stars: 22 - Forks: 5
AmayaGS/WSI_Segmentation
Automated segmentation of H&E and Immunohistochemistry stained synovial tissue in histopathology Whole Slide Images - MIUA 2023
Language: Python - Size: 3.08 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
TatjanaChernenko/word_sense_induction_CHERTOY_system
An approach to improve word sense induction systems (WSI) for web search result clustering. Exploring the boundaries of vector space models for the WSI Task. CHERTOY system. Chernenko, Tatjana and Toyota, Utaemon Institute for Computational Linguistics of University Heidelberg. 2017/2018
Language: Python - Size: 723 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
namandangi/wsi
Image Processing and CV on Whole Slide Images
Language: Jupyter Notebook - Size: 8.82 MB - Last synced at: 27 days ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 1
constantjxyz/GC-SPLeM
Survival Prediction for Gastric Cancer via Multimodal Learning of Whole Slide Images and Gene Expression -- BIBM 2022
Language: Python - Size: 66.4 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 0
cylab-tw/raccoon
Raccoon is a NoSQL-based medical image archive for managing the DICOM images.
Language: JavaScript - Size: 24.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 45 - Forks: 10
seycho/python_mini_script-LoRA_WSI
LoRA training code with TCGA-LUAD WSI
Language: Python - Size: 310 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
seycho/WSI_Preprocess
Whole Slide Image mask preprocessing modules.
Language: Jupyter Notebook - Size: 41.6 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 1 - 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: 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
artreven/thesaural_wsi
Data for discrimination of word senses using hypernyms
Size: 17.9 MB - Last synced at: almost 2 years ago - Pushed at: almost 8 years ago - Stars: 2 - Forks: 1
pathologyatlas/mucin
mucicarmine histochemistry stain showing intracellular mucin in a normal colon
Language: JavaScript - Size: 202 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
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
Zhengyushan/kat
The code for Kernel attention transformer (KAT)
Language: Python - Size: 278 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 19 - Forks: 1
kimdesok/DeepPATH Fork of ncoudray/DeepPATH
AI HUB Project: Classification of Lung Cancer Slide Images using Deep-Learning
Language: Jupyter Notebook - Size: 25.9 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
Jiawei-Yang/Few-shot-WSI
[ICLR2022] This project hosts the code for the paper: Towards Better Understanding and Better Generalization of Low-shot Classification in Histology Images with Contrastive Learning.
Language: Python - Size: 6.94 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 11 - 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
yasohasakii/WSI-SDK
Toolkit for WSI preprocess, such as resample & zoom, mask, roi selection ect.
Language: Python - Size: 881 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 9 - Forks: 8
tcxxxx/WSI-analysis
Python scripts for automatic Whole-Slide Image preprocessing.
Language: HTML - Size: 4.45 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 31 - Forks: 13
IAmS4n/HEROHE
Implementation of Piaze Team for HEROHE challenge
Language: Python - Size: 14.1 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0
skoc/wsi-heatmap
WSI Clustering Heatmap with ResNet Features
Language: Python - Size: 13.5 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0
smujiang/WSI2DICOM
Simple prototype of converting whole slide image (WSI) to multiframe DICOM images
Language: Python - Size: 7.99 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 10 - 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
asafamr/bertwsi
Word Sense Induction with BERT MLM
Language: Python - Size: 21.5 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 28 - Forks: 8
PingjunChen/ThyroidRule
Rule-Based Thyroid Whole Slide Image Diagnosis
Language: Python - Size: 429 KB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 8 - Forks: 1
Zhengyushan/lagenet
The code for LAGE-Net
Language: Python - Size: 38.1 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 8 - Forks: 2
bartlomiejkrawczyk/WSI-21Z
Introduction to Artificial Intelligence - laboratories at the Warsaw University of Technology
Language: Python - Size: 6.54 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0
IAmS4n/TensorBoard_Plugin_WSI
A plugin for TensorBoard to show WSI images. The plugin is based on Deep Zoom Image (DZI).
Language: JavaScript - Size: 1.26 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0
PingjunChen/ThyroidInteractive
Suspicious Regions-Based Whole Slide Image Analysis
Language: Python - Size: 4.09 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 2
waynewccheng/pca
Principle component analysis with Biomax samples
Language: HTML - Size: 1.17 GB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
waynewccheng/OL490_PR730_QE65
Measurement data in comparison with QE65 after PR730 calibration
Language: MATLAB - Size: 3.14 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1