Open source tools for computational pathology - Nature BME

QuPath - Open-source bioimage analysis for research

Hierarchical Image Pyramid Transformer - CVPR 2022 (Oral)

Tools for computational pathology

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

Towards a general-purpose foundation model for computational pathology - Nature Medicine

Tools for tissue image stain normalisation and augmentation in Python 3

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

Powerful, open-source AI tools for digital pathology.

HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024 (Spotlight)

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)

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

Stain normalization tools for histological analysis and computational pathology

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)

[CVPR'23] Histopathology Whole Slide Image Analysis with Heterogeneous Graph Representation Learning

This is the official repository for our CVPR 2023 paper 'Task-Specific Fine-Tuning via Variational Information Bottleneck for Weakly-Supervised Pathology Whole Slide Image Classification'.