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

Continuum modelling and simulation of granular flows through their many phases

We propose and numerically implement a constitutive framework for granular media that allows the material to traverse through its many common phases during the flow process. When dense, the material is treated as a pressure sensitive elasto-viscoplastic solid obeying a yield criterion and a plastic flow rule given by the $\mu(I)$ inertial rheology of granular materials. When the free volume exceeds a critical level, the material is deemed to separate and is treated as disconnected, stress-free media. A Material Point Method (MPM) procedure is written for the simulation of this model and many demonstrations are provided in different geometries. By using the MPM framework, extremely large strains and nonlinear deformations, which are common in granular flows, are representable. The method is verified numerically and its physical predictions are validated against known results

Conformational Dynamics of Supramolecular Protein Assemblies in the EMDB

The Electron Microscopy Data Bank (EMDB) is a rapidly growing repository for the dissemination of structural data from single-particle reconstructions of supramolecular protein assemblies including motors, chaperones, cytoskeletal assemblies, and viral capsids. While the static structure of these assemblies provides essential insight into their biological function, their conformational dynamics and mechanics provide additional important information regarding the mechanism of their biological function. Here, we present an unsupervised computational framework to analyze and store for public access the conformational dynamics of supramolecular protein assemblies deposited in the EMDB. Conformational dynamics are analyzed using normal mode analysis in the finite element framework, which is used to compute equilibrium thermal fluctuations, cross-correlations in molecular motions, and strain energy distributions for 452 of the 681 entries stored in the EMDB at present. Results for the viral capsid of hepatitis B, ribosome-bound termination factor RF2, and GroEL are presented in detail and validated with all-atom based models. The conformational dynamics of protein assemblies in the EMDB may be useful in the interpretation of their biological function, as well as in the classification and refinement of EM-based structures.Comment: Associated online data bank available at: http://lcbb.mit.edu/~em-nmdb

DeepSketch2Face: A Deep Learning Based Sketching System for 3D Face and Caricature Modeling

Face modeling has been paid much attention in the field of visual computing. There exist many scenarios, including cartoon characters, avatars for social media, 3D face caricatures as well as face-related art and design, where low-cost interactive face modeling is a popular approach especially among amateur users. In this paper, we propose a deep learning based sketching system for 3D face and caricature modeling. This system has a labor-efficient sketching interface, that allows the user to draw freehand imprecise yet expressive 2D lines representing the contours of facial features. A novel CNN based deep regression network is designed for inferring 3D face models from 2D sketches. Our network fuses both CNN and shape based features of the input sketch, and has two independent branches of fully connected layers generating independent subsets of coefficients for a bilinear face representation. Our system also supports gesture based interactions for users to further manipulate initial face models. Both user studies and numerical results indicate that our sketching system can help users create face models quickly and effectively. A significantly expanded face database with diverse identities, expressions and levels of exaggeration is constructed to promote further research and evaluation of face modeling techniques.Comment: 12 pages, 16 figures, to appear in SIGGRAPH 201

Morphological shape generation through user-controlled group metamorphosis

Morphological shape design is interpreted in this paper as a search for new shapes from a particular application domain represented by a set of selected shape instances. This paper proposes a new foundation for morphological shape design and generation. In contrast to existing generative procedures, an approach based on a user-controlled metamorphosis between functionally based shape models is presented. A formulation of the pairwise metamorphosis is proposed with a variety of functions described for the stages of deformation, morphing and offsetting. This formulation is then extended to the metamorphosis between groups of shapes with user-defined, dynamically correlated and weighted feature elements. A practical system was implemented in the form of plugin to Maya and tested by an industrial designer on a group of representative shapes from a particular domain. © 2013 Elsevier Ltd