Repository Index

AI Toolkit for Healthcare Imaging

• healthcare-imaging
• deep-learning
• medical-image-computing
• medical-image-processing

This repository includes the official project of TransUNet, presented in our paper: TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation.

Unsupervised Learning for Image Registration

• image-registration
• image-alignment
• machine-learning
• deep-learning

Multi-platform, free open source software for visualization and image computing.

• medical-imaging
• vtk
• itk
• python

Semi Supervised Learning for Medical Image Segmentation, a collection of literature reviews and code implementations.

• semi-supervised-learning

Medical imaging processing for AI applications.

• pytorch
• medical-image-computing
• deep-learning
• data-augmentation

Many studies have shown that the performance on deep learning is significantly affected by volume of training data. The MedicalNet project provides a series of 3D-ResNet pre-trained models and relative code.

Pytorch 3D U-Net Convolution Neural Network (CNN) designed for medical image segmentation

Read, modify and write DICOM files with python code

• dicom
• pydicom
• python

[Deprecated] Use Cornerstone3D Instead https://cornerstonejs.org/

• javascript
• cornerstone
• dicom
• medical-imaging

TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.

• medical-imaging
• medical-ai
• deep-learning
• machine-learning

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab

Clinical Histopathology Imaging Evaluation Foundation Model

Prov-GigaPath: A whole-slide foundation model for digital pathology from real-world data

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model

Dicoogle - Open Source PACS

• dicoogle
• dicom
• pacs
• medical-imaging

C library for reading virtual slide images

• pathology
• whole-slide-imaging
• c

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.

• histopathology-images
• microscopy
• sliding-windows
• medical-image-analysis

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing

Pathology Language and Image Pre-Training (PLIP) is the first vision and language foundation model for Pathology AI (Nature Medicine). PLIP is a large-scale pre-trained model that can be used to extract visual and language features from pathology images and text description. The model is a fine-tuned version of the original CLIP model.

• artificial-intelligence
• clip
• pathology
• vision-and-language

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.

• hubmap
• imaging
• openmicroscopy
• ome-tiff

Image restoration for fluorescence microscopy

Kaapana is an open source toolkit for state of the art platform provisioning in the field of medical data analysis. The applications comprise AI-based workflows and federated learning scenarios with a focus on radiological and radiotherapeutic imaging. The name Kaapana comes from the Hawaiian word kaʻāpana, meaning "distributor" or "part".

• imaging
• ai
• cloud-computing
• medical-imaging

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

• histology
• wsi-images
• pan-cancer-analysis
• genomics