Open source tools for computational pathology - Nature BME

QuPath - Open-source bioimage analysis for research

Hierarchical Image Pyramid Transformer - CVPR 2022 (Oral)

A general-purpose foundation model for computational pathology - Nature Medicine

Tools for computational pathology

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

A vision-language foundation model for computational pathology - Nature Medicine

Tools for tissue image stain normalisation and augmentation in Python 3

Powerful, open-source AI tools for digital pathology.

A toolkit for integrating histology and spatial transcriptomics - NeurIPS 2024

Code associated to the publication: Scaling self-supervised learning for histopathology with masked image modeling, A. Filiot et al., MedRxiv (2023). We publicly release Phikon 🚀

Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology (LMRL Workshop, NeurIPS 2021)

Stain normalization tools for histological analysis and computational pathology

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

⚡ Open-source software for deep learning-based digital pathology

List of pathology feature extractors and foundation models

Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images - CVPR 2023

A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.

HistoSegNet: Semantic Segmentation of Histological Tissue Type in Whole Slide Images (ICCV 2019)

One Model is All You Need: Multi-Task Learning Enables Simultaneous Histology Image Segmentation and Classification