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Histopathology Image Analysis
Notebooks for working with The Cancer Imaging Archive datasets. Have you written one? Submit a PR!
Interactive image stack viewing in jupyter notebooks based on ipycanvas and ipywidgets
[CVPR2024] Self-Supervised Vision Mamba for Histopathology Images
Various scripts written for image analysis utilities
an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.
Omnipose: a high-precision solution for morphology-independent cell segmentation
This repository contains all files for the BioProtocols submission (DOI: 10.21769/BioProtoc.4776). Included are scripts for automated quantification of whole-slide scanned liver sections for the pu…
Analysis of 3D pathology samples using weakly supervised AI - Cell
nuclei.io: Human-in-the-loop active learning framework for pathology image analysis
HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024 (Spotlight)
Model Weights for the ISGPP model for the segmentation of Pancreatic Ductal Adenocarcinoma (PDAC) after neoadjuvant therapy
A python based GUI to annotate images and save annotations as COCO style JSON format.
This script takes whole slide images (typically .svs or .ndpi files; either from biospsies or Cytosponge etc) as an input and returns an image file (typically .png file) of the mask of where the ti…
Template to help create a new QuPath extension
Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration
A basic analysis on SVS images using OpenSlide. This project's main focus is storage cost of whole-slide image data using different image format, but it can change to something else.
Python Whole Slide Image Preprocessing
A deep learning approach to predicting breast tumor proliferation scores for the TUPAC16 challenge
Unsupervised Semantic Segmentation for Pathology
The official QuPath extension for InstanSeg