elastix

Elastix is an open-source software package for medical image registration. It is designed to align images acquired under different conditions, times, or modalities, and supports two- and three-dimensional data. The toolbox provides rigid, affine, and deformable (nonrigid) registration, including B-spline based transforms for flexible alignment.

The software is built on the ITK framework and follows a modular pipeline approach. Registration workflows are configured via text parameter files that specify components such as similarity metrics (for example, mutual information, normalized cross-correlation, or correlation ratio), optimizers, sampling schemes, and multi-resolution strategies. This parameter-driven design allows users to assemble and customize registration pipelines without writing code.

Elastix operates in two main stages. Elastix performs the registration and outputs a transform parameter file describing the spatial mapping between images. A companion tool, transformix, can then apply the resulting transform to images, label maps, or other data to generate resampled outputs in a common coordinate system. The package supports multi-modal registration and a range of imaging modalities common in clinical and research settings.

Applications and availability: Elastix is widely used in medical imaging research for tasks such as atlas-based segmentation, image-guided therapy planning, and longitudinal studies. It is distributed as open-source software, with ongoing development and documentation, and integrates with other ITK-based tools and workflows across platforms.