Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i

BSP-fields: An Exact Representation of Polygonal Objects by Differentiable Scalar Fields Based on Binary Space Partitioning

The problem considered in this work is to find a dimension independent algorithm for the generation of signed scalar fields exactly representing polygonal objects and satisfying the following requirements: the defining real function takes zero value exactly at the polygonal object boundary; no extra zero-value isosurfaces should be generated; C1 continuity of the function in the entire domain. The proposed algorithms are based on the binary space partitioning (BSP) of the object by the planes passing through the polygonal faces and are independent of the object genus, the number of disjoint components, and holes in the initial polygonal mesh. Several extensions to the basic algorithm are proposed to satisfy the selected optimization criteria. The generated BSP-fields allow for applying techniques of the function-based modeling to already existing legacy objects from CAD and computer animation areas, which is illustrated by several examples

Mesh modification using deformation gradients

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. 117-131).Computer-generated character animation, where human or anthropomorphic characters are animated to tell a story, holds tremendous potential to enrich education, human communication, perception, and entertainment. However, current animation procedures rely on a time consuming and difficult process that requires both artistic talent and technical expertise. Despite the tremendous amount of artistry, skill, and time dedicated to the animation process, there are few techniques to help with reuse. Although individual aspects of animation are well explored, there is little work that extends beyond the boundaries of any one area. As a consequence, the same procedure must be followed for each new character without the opportunity to generalize or reuse technical components. This dissertation describes techniques that ease the animation process by offering opportunities for reuse and a more intuitive animation formulation. A differential specification of arbitrary deformation provides a general representation for adapting deformation to different shapes, computing semantic correspondence between two shapes, and extrapolating natural deformation from a finite set of examples.(cont.) Deformation transfer adds a general-purpose reuse mechanism to the animation pipeline by transferring any deformation of a source triangle mesh onto a different target mesh. The transfer system uses a correspondence algorithm to build a discrete many-to-many mapping between the source and target triangles that permits transfer between meshes of different topology. Results demonstrate retargeting both kinematic poses and non-rigid deformations, as well as transfer between characters of different topological and anatomical structure. Mesh-based inverse kinematics extends the idea of traditional skeleton-based inverse kinematics to meshes by allowing the user to pose a mesh via direct manipulation. The user indicates the dass of meaningful deformations by supplying examples that can be created automatically with deformation transfer, sculpted, scanned, or produced by any other means. This technique is distinguished from traditional animation methods since it avoids the expensive character setup stage. It is distinguished from existing mesh editing algorithms since the user retains the freedom to specify the class of meaningful deformations. Results demonstrate an intuitive interface for posing meshes that requires only a small amount of user effort.by Robert Walker Sumner.Ph.D

Template-free Articulated Neural Point Clouds for Reposable View Synthesis

Dynamic Neural Radiance Fields (NeRFs) achieve remarkable visual quality when synthesizing novel views of time-evolving 3D scenes. However, the common reliance on backward deformation fields makes reanimation of the captured object poses challenging. Moreover, the state of the art dynamic models are often limited by low visual fidelity, long reconstruction time or specificity to narrow application domains. In this paper, we present a novel method utilizing a point-based representation and Linear Blend Skinning (LBS) to jointly learn a Dynamic NeRF and an associated skeletal model from even sparse multi-view video. Our forward-warping approach achieves state-of-the-art visual fidelity when synthesizing novel views and poses while significantly reducing the necessary learning time when compared to existing work. We demonstrate the versatility of our representation on a variety of articulated objects from common datasets and obtain reposable 3D reconstructions without the need of object-specific skeletal templates. Code will be made available at https://github.com/lukasuz/Articulated-Point-NeRF

Reconstructing triangulated surfaces from unorganized points through local skeletal stars

Surface reconstruction from unorganized points arises in a variety of practical situations such as range scanning an object from multiple view points, recovery of biological shapes from twodimensional slices, and interactive surface sketching. [...]Reconstrução da superfície de pontos desorganizados surge em uma variedade de situações práticas, tais como rastreamento de um objeto a partir de vários pontos de vista, a recuperação de formas biológicas de fatias bi-dimensionais, e esboçar superfícies interativas. [...

Doctor of Philosophy

dissertationShape analysis is a well-established tool for processing surfaces. It is often a first step in performing tasks such as segmentation, symmetry detection, and finding correspondences between shapes. Shape analysis is traditionally employed on well-sampled surfaces where the geometry and topology is precisely known. When the form of the surface is that of a point cloud containing nonuniform sampling, noise, and incomplete measurements, traditional shape analysis methods perform poorly. Although one may first perform reconstruction on such a point cloud prior to performing shape analysis, if the geometry and topology is far from the true surface, then this can have an adverse impact on the subsequent analysis. Furthermore, for triangulated surfaces containing noise, thin sheets, and poorly shaped triangles, existing shape analysis methods can be highly unstable. This thesis explores methods of shape analysis applied directly to such defect-laden shapes. We first study the problem of surface reconstruction, in order to obtain a better understanding of the types of point clouds for which reconstruction methods contain difficulties. To this end, we have devised a benchmark for surface reconstruction, establishing a standard for measuring error in reconstruction. We then develop a new method for consistently orienting normals of such challenging point clouds by using a collection of harmonic functions, intrinsically defined on the point cloud. Next, we develop a new shape analysis tool which is tolerant to imperfections, by constructing distances directly on the point cloud defined as the likelihood of two points belonging to a mutually common medial ball, and apply this for segmentation and reconstruction. We extend this distance measure to define a diffusion process on the point cloud, tolerant to missing data, which is used for the purposes of matching incomplete shapes undergoing a nonrigid deformation. Lastly, we have developed an intrinsic method for multiresolution remeshing of a poor-quality triangulated surface via spectral bisection