Repository Index

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

Tool for robust segmentation of >100 important anatomical structures in CT and MR images

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

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

Use of Attention Gates in a Convolutional Neural Network / Medical Image Classification and Segmentation

• convolutional-neural-networks
• attention-model
• image-classification
• image-segmentation

Train AI models efficiently on medical images using any framework

• pytorch
• deep-learning
• keras
• neuroimaging

DICOM Web Viewer: open source zero footprint medical image library.

• dicom
• medical-imaging
• zero-footprint
• viewer

Open source tools for computational pathology - Nature BME

• histopathology
• pathology
• weakly-supervised-learning
• whole-slide-imaging

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

• itk
• insight-toolkit
• image-analysis
• medical-imaging

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab

A pure JavaScript medical research image viewer.

Vision-Language Pathology Foundation Model - Nature Medicine

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

Dicoogle - Open Source PACS

• dicoogle
• dicom
• pacs
• medical-imaging

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

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

Neural networks toolbox focused on medical image analysis

• python
• keras
• convolutional-neural-networks
• brain

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

Azure friendly DICOMweb part 18 .NET server with qido-rs, wado-rs, stow-rs, wado-uri RESTful implementation

• dicom
• dicomweb
• dicomcloud
• wado

Automated 3D cell detection in very large images

• microscopy
• cell-detection
• deep-learning
• image-analysis

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

• cancer-imaging-research
• radiomics
• radiomics-features
• machine-learning

A Python interface to access neuroanatomical atlases

• neuroscience
• python
• microscopy
• registration

AI-based pathology predicts origins for cancers of unknown primary - Nature

• histology
• pathology
• wsi-images
• histopathology

Automated 3D brain registration with support for multiple species and atlases.

• registration
• atlases
• brain
• neuroscience