computational-pathology

Open source tools for computational pathology - Nature BME

QuPath - Open-source bioimage analysis for research

Hierarchical Image Pyramid Transformer - CVPR 2022 (Oral)

Pathology Foundation Model - Nature Medicine

Tools for computational pathology

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

Vision-Language Pathology Foundation Model - Nature Medicine

Tools for tissue image stain normalisation and augmentation in Python 3

Powerful, open-source AI tools for digital pathology.

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 🚀

Stain normalization tools for histological analysis and computational pathology

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

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)

Attention-Challenging Multiple Instance Learning for Whole Slide Image Classification (ECCV2024)