Placental Flattening via Volumetric Parameterization

We present a volumetric mesh-based algorithm for flattening the placenta to a canonical template to enable effective visualization of local anatomy and function. Monitoring placental function in vivo promises to support pregnancy assessment and to improve care outcomes. We aim to alleviate visualization and interpretation challenges presented by the shape of the placenta when it is attached to the curved uterine wall. To do so, we flatten the volumetric mesh that captures placental shape to resemble the well-studied ex vivo shape. We formulate our method as a map from the in vivo shape to a flattened template that minimizes the symmetric Dirichlet energy to control distortion throughout the volume. Local injectivity is enforced via constrained line search during gradient descent. We evaluate the proposed method on 28 placenta shapes extracted from MRI images in a clinical study of placental function. We achieve sub-voxel accuracy in mapping the boundary of the placenta to the template while successfully controlling distortion throughout the volume. We illustrate how the resulting mapping of the placenta enhances visualization of placental anatomy and function. Our code is freely available at https://github.com/mabulnaga/placenta-flattening .Comment: MICCAI 201

Structural Analysis: Shape Information via Points-To Computation

This paper introduces a new hybrid memory analysis, Structural Analysis, which combines an expressive shape analysis style abstract domain with efficient and simple points-to style transfer functions. Using data from empirical studies on the runtime heap structures and the programmatic idioms used in modern object-oriented languages we construct a heap analysis with the following characteristics: (1) it can express a rich set of structural, shape, and sharing properties which are not provided by a classic points-to analysis and that are useful for optimization and error detection applications (2) it uses efficient, weakly-updating, set-based transfer functions which enable the analysis to be more robust and scalable than a shape analysis and (3) it can be used as the basis for a scalable interprocedural analysis that produces precise results in practice. The analysis has been implemented for .Net bytecode and using this implementation we evaluate both the runtime cost and the precision of the results on a number of well known benchmarks and real world programs. Our experimental evaluations show that the domain defined in this paper is capable of precisely expressing the majority of the connectivity, shape, and sharing properties that occur in practice and, despite the use of weak updates, the static analysis is able to precisely approximate the ideal results. The analysis is capable of analyzing large real-world programs (over 30K bytecodes) in less than 65 seconds and using less than 130MB of memory. In summary this work presents a new type of memory analysis that advances the state of the art with respect to expressive power, precision, and scalability and represents a new area of study on the relationships between and combination of concepts from shape and points-to analyses

Unwind: Interactive Fish Straightening

The ScanAllFish project is a large-scale effort to scan all the world's 33,100 known species of fishes. It has already generated thousands of volumetric CT scans of fish species which are available on open access platforms such as the Open Science Framework. To achieve a scanning rate required for a project of this magnitude, many specimens are grouped together into a single tube and scanned all at once. The resulting data contain many fish which are often bent and twisted to fit into the scanner. Our system, Unwind, is a novel interactive visualization and processing tool which extracts, unbends, and untwists volumetric images of fish with minimal user interaction. Our approach enables scientists to interactively unwarp these volumes to remove the undesired torque and bending using a piecewise-linear skeleton extracted by averaging isosurfaces of a harmonic function connecting the head and tail of each fish. The result is a volumetric dataset of a individual, straight fish in a canonical pose defined by the marine biologist expert user. We have developed Unwind in collaboration with a team of marine biologists: Our system has been deployed in their labs, and is presently being used for dataset construction, biomechanical analysis, and the generation of figures for scientific publication

VOLMAP: a Large Scale Benchmark for Volume Mappings to Simple Base Domains

Correspondences between geometric domains (mappings) are ubiquitous in computer graphics and engineering, both for a variety of downstream applications and as core building blocks for higher level algorithms. In particular, mapping a shape to a convex or star-shaped domain with simple geometry is a fundamental module in existing pipelines for mesh generation, solid texturing, generation of shape correspondences, advanced manufacturing etc. For the case of surfaces, computing such a mapping with guarantees of injectivity is a solved problem. Conversely, robust algorithms for the generation of injective volume mappings to simple polytopes are yet to be found, making this a fundamental open problem in volume mesh processing. VOLMAP is a large scale benchmark aimed to support ongoing research in volume mapping algorithms. The dataset contains 4.7K tetrahedral meshes, whose boundary vertices are mapped to a variety of simple domains, either convex or star-shaped. This data constitutes the input for candidate algorithms, which are then required to position interior vertices in the domain to obtain a volume map. Overall, this yields more than 22K alternative test cases. VOLMAP also comprises tools to process this data, analyze the resulting maps, and extend the dataset with new meshes, boundary maps and base domains. This article provides a brief overview of the field, discussing its importance and the lack of effective techniques. We then introduce both the dataset and its major features. An example of comparative analysis between two existing methods is also present