ANTsX/ANTsR

Advanced Normalization Tools (ANTs)

A fast medical imaging analysis library in Python with algorithms for registration, segmentation, and more.

SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.

Deep learning for medical images in R: semantic and instance segmentation, object detection, 2D and 3D, DICOM and NIfTI, one specification.

R package for structural neuroimaging. Provides high-level functions to access (read and write) and visualize surface-based brain morphometry data for individuals and groups.

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.

An ITK Python interface to elastix, a toolbox for rigid and nonrigid registration of images

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.