Ressources of histopathology datasets

Federated Learning for Computational Pathology - Medical Image Analysis

PyTorch implementation of Learning to Downsample for Segmentation of Ultra-High Resolution Images [ICLR 2022]

HistoSeg is an Encoder-Decoder DCNN which utilizes the novel Quick Attention Modules and Multi Loss function to generate segmentation masks from histopathological images with greater accuracy. This repo contains the code to Test and Train the HistoSeg

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io)

Fine-grained Spatial Transcriptomics by integrating paired histology image

CODAvision - open source medical image labeling tool

Automated liver NAFLD/NASH scoring

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

MICCAI25 | MiCo: Multiple Instance Learning with Context-Aware Clustering for Whole Slide Image Analysis

Training a local neural network from multiple MRI to histology

Complete Matlab pipeline for matching in vivo recorded cells post hoc in histology

Pytorch implementation of NEGEV method. Paper: "Negative Evidence Matters in Interpretable Histology Image Classification".

CUCA: Predicting fine-grained cell types from histology images through cross-modal learning in spatial transcriptomics

DisCo: Consolidating Dispersed Semantics via Context-Aware Clustering for Whole Slide Images Analysis

Constrained self-supervised method with temporal ensembling for fiber bundle detection on anatomic tracing data

Atelier3D wiki

Deep-learning based classification pipeline for subtyping lung tumors from histology. Study design and codebase to analyze the impact of nucleus segmentation on subtyping.

SectraPlugin Frontend — Flutter web for PACS histology image analysis plugin (Flutter - Docker - Nginx) | HES-SO student bachelor thesis project 2024

Quantifying predictability of gene expression from histology image