Repository Index

AI Toolkit for Healthcare Imaging

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

OHIF zero-footprint DICOM viewer and oncology specific Lesion Tracker, plus shared extension packages

• nci-itcr
• nci-qin
• quantitative-imaging
• imaging-informatics

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

• medical-imaging
• vtk
• itk
• python

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

• javascript
• cornerstone
• dicom
• medical-imaging

Fellow Oak DICOM for .NET, .NET Core, Universal Windows, Android, iOS, Mono and Unity

• dicom
• netcore
• medical
• medical-imaging

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab

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

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

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

Medical LLM agent and MRI segmentation workspace built on PharmaLLM, with LangGraph, vLLM, and BEU-Net.

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

Interoperable web-based DICOM slide microscopy viewer and annotation tool

• dicomweb
• oidc
• react
• digital-pathology

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

• registration
• atlases
• brain
• neuroscience

⚡ Open-source software for deep learning-based digital pathology

• deep-learning
• machine-learning
• digital-pathology
• computational-pathology

ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data

• neuroimaging
• reproducibility
• pipeline
• meta-analysis

Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.

• minerva
• microscopy
• ome
• immunofluorescence

A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources

• bioimage-analysis
• cell-classification
• computer-vision
• digital-pathology

mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance

• qa
• mri
• neuroimaging
• niqc

Functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats.

• nifti
• afni
• analyze

a collection of small utlities useful for neuroimaging research

• utilities