CLAIRE -- Parallelized Diffeomorphic Image Registration for Large-Scale Biomedical Imaging Applications

We study the performance of CLAIRE -- a diffeomorphic multi-node, multi-GPU image-registration algorithm, and software -- in large-scale biomedical imaging applications with billions of voxels. At such resolutions, most existing software packages for diffeomorphic image registration are prohibitively expensive. As a result, practitioners first significantly downsample the original images and then register them using existing tools. Our main contribution is an extensive analysis of the impact of downsampling on registration performance. We study this impact by comparing full-resolution registrations obtained with CLAIRE to lower-resolution registrations for synthetic and real-world imaging datasets. Our results suggest that registration at full resolution can yield a superior registration quality -- but not always. For example, downsampling a synthetic image from $1024^3$ to $256^3$ decreases the Dice coefficient from 92% to 79%. However, the differences are less pronounced for noisy or low-contrast high-resolution images. CLAIRE allows us not only to register images of clinically relevant size in a few seconds but also to register images at unprecedented resolution in a reasonable time. The highest resolution considered is CLARITY images of size $2816\times3016\times1162$. To the best of our knowledge, this is the first study on image registration quality at such resolutions.Comment: 32 pages, 9 tables, 8 figure

Editing Fluid Simulations with Jet Particles

Fluid simulation is an important topic in computer graphics in the pursuit of adding realism to films, video games and virtual environments. The results of a fluid simulation are hard to edit in a way that provide a physically plausible solution. Edits need to preserve the incompressibility condition in order to create natural looking water and smoke simulations. In this thesis we present an approach that allows a simple artist-friendly interface for designing and editing complex fluid-like flows that are guaranteed to be incompressible in two and three dimensions. Key to our method is a formulation for the design of flows using jet particles. Jet particles are Lagrangian solutions to a regularised form of Euler’s equations, and their velocity fields are divergence-free which motivates their use in computer graphics. We constrain their dynamics to design divergence-free flows and utilise them effectively in a modern visual effects pipeline. Using just a handful of jet particles we produce visually convincing flows that implicitly satisfy the incompressibility condition. We demonstrate an interactive tool in two dimensions for designing a range of divergence-free deformations. Further we describe methods to couple these flows with existing simulations in order to give the artist creative control beyond the initial outcome. We present examples of local temporal edits to smoke simulations in 2D and 3D. The resulting methods provide promising new ways to design and edit fluid-like deformations and to create general deformations in 3D modelling. We show how to represent existing divergence-free velocity fields using jet particles, and design new vector fields for use in fluid control applications. Finally we provide an efficient implementation for deforming grids, meshes, volumes, level sets, vectors and tensors, given a jet particle flow