Open source tools for computational pathology - Nature BME

QuPath - Open-source bioimage analysis for research

Pathology Foundation Model - Nature Medicine

Hierarchical Image Pyramid Transformer - CVPR 2022 (Oral)

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

Vision-Language Pathology Foundation Model - Nature Medicine

Tools for computational pathology

Integrating histology and spatial transcriptomics - NeurIPS 2024

Powerful, open-source AI tools for digital pathology.

Tools for tissue image stain normalisation and augmentation in Python 3

Multimodal Whole Slide Foundation Model for Pathology

Stain normalization tools for histological analysis and computational pathology

List of pathology feature extractors and foundation models

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

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

The official implementation of GPFM

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.

Awesome List of Digital and Computational Pathology Resources

Multimodal fusion for heterogeneous biomedical data. NeurIPS 2024.

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

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

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

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'.

A pipeline to segment tissue from the background in histological images

Interpretable Vision-Language Survival Analysis with Ordinal Inductive Bias for Computational Pathology (ICLR 2025)

DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xenium) resolution.