Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]

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

Image data augmentation on-the-fly by add new class on transforms in PyTorch and torchvision.

Contextual Attention Network: Transformer Meets U-Net

BIRL: Benchmark on Image Registration methods with Landmark validations

BrainPainter - Brain Visualisation Software

A Large Language-Vision Assistant for Pathology Image Understanding (BIBM-2024 & Journal of Artificial Intelligence Review 2025)

:microscope: Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.

Scripts for https://www.nature.com/articles/s41598-018-27707-4, using Convolutional Neural Network to detect lung cancer tumor area

Whole Slide Digital Pathology Image Tissue Localization

The code for Kernel attention transformer (KAT)

Predicting gastric cancer outcome from resected lymph node histopathology images using deep learning

Preprocessing module for large histological images

A curated list of awesome Multi-instance Learning frameworks for Whole Slide Images (WSIs) classification, segmentation, etc.

[IEEE TMI 2025] MIRROR: Multi-Modal Pathological Self-Supervised Representation Learning via Modality Alignment and Retention

LabelSlide is a slide annotation tool and label object bounding boxes in virtual slides (generally used in pathology)

AEM: Attention Entropy Maximization for Multiple Instance Learning based Whole Slide Image Classification

Simple prototype of converting whole slide image (WSI) to multiframe DICOM images

H&E ROI-Level and WSI-Level Nuclei Segmentation with HoVer-Net

Noise Robust Learning with Hard Example Aware for Pathological Image classification

The nuclei detection method on histology image proposed in the 2017 paper by Peikari et al.

Compact Self-Supervised Vision Transformer (cSiT) on Histopathology Images

A collection of groovy scripts for digital pathology

Macenko normalisation of big medical slides

In the dynamic landscape of medical artificial intelligence, this study explores the vulnerabilities of the Pathology Language-Image Pretraining (PLIP) model, a Vision Language Foundation model, under targeted attacks like PGD adversarial attack.

MMIR: Multimodal Image Registration

Python library for pathology image analysis

Lung Preneoplasia Progression via Pathomics

A multi-resolution CNN package to predict endometrial cancer features