Multi-object geodesic active contours (MOGAC).

An emerging topic is to build image segmentation systems that can segment hundreds to thousands of objects (i.e. cell segmentation\tracking, full brain parcellation, full body segmentation, etc.

Multi-object spring level sets (MUSCLE).

A new data structure is presented for geometrically modeling multi-objects. The model can exhibit elastic and fluid-like behavior to enable interpretability between tasks that require both deformable registration and active contour segmentation. The data structure consists of a label mask, distance field, and springls (a constellation of disconnected triangles).

Spring level sets: a deformable model representation to provide interoperability between meshes and level sets.

A new type of deformable model is presented that merges meshes and level sets into one representation to provide interoperability between methods designed for either. This includes the ability to circumvent the CFL time step restriction for methods that require large step sizes. The key idea is to couple a constellation of disconnected triangular surface elements (springls) with a level set that tracks the moving constellation.

An active contour method for bone cement reconstruction from C-arm x-ray images.

A novel algorithm is presented to segment and reconstruct injected bone cement from a sparse set of X-ray images acquired at arbitrary poses. The sparse X-ray multi-view active contour (SxMAC-pronounced "smack") can 1) reconstruct objects for which the background partially occludes the object in X-ray images, 2) use X-ray images acquired on a noncircular trajectory, and 3) incorporate prior computed tomography (CT) information. The algorithm's inputs are preprocessed X-ray images, their associated pose information, and prior CT, if available.

SpringLS: a deformable model representation to provide interoperability between meshes and level sets.

A new type of deformable model is presented that merges meshes and level sets into one representation to provide interoperability between methods designed for either. The key idea is to use a constellation of triangular surface elements (springls) to define a level set. A Spring Level Set (SpringLS) can be interpreted as a mesh or level set and used in place of them in many instances.

The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software.

Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms.