software

ITK-SNAP (home, code) is an interactive open-source tool for medical image segmentation. It has over 10000 monthly downloads and is used by hundreds of research groups around the world.

Automatic Segmentation of Hippocampal Subfields (ASHS) (home, code) and the new version HyperResASHS (home)) is a tool for automatic segmentation of the medial temporal lobe (MTL) substructures from brain MRI scans. These structures are involved in early Alzheimer's disease and in a number of other neurological conditions. They are also important in research on memory and cognition.

purple-mri (home, code) is a comprehensive package for automatic segmentation, surface-based anatomical parcellation, and groupwise registration of ultra-high-resolution postmortem MRI of human brain hemispheres. This tool allows these images to be processed using FreeSurfer-based pipelines.

PICSL Histology Annotation System / PHAS (home, docs, demo) is a web-based large-scale digital histopathology image archive and a platform for annotation and training deep learning classifiers. It allows annotation to be easily crowdsourced with a centralized data repository.

Convert3D / C3D (home, code, python wrapper) is a commmand-line image processing tool that offers complementary features to ITK-SNAP. Originally developed to convert between various 3D image formats, the tool has become more of a Swiss army knife for medical image processing.

Greedy (home, code, python wrapper) is a tool for fast medical image registration. The motivation for developing greedy was to have a really fast CPU-based deformable image registration tool that could be used in applications and pipelines where many images have to be registered in parallel.