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

Curve Skeleton and Moments of Area Supported Beam Parametrization in Multi-Objective Compliance Structural Optimization

This work addresses the end-to-end virtual automation of structural optimization up to the derivation of a parametric geometry model that can be used for application areas such as additive manufacturing or the verification of the structural optimization result with the finite element method. A holistic design in structural optimization can be achieved with the weighted sum method, which can be automatically parameterized with curve skeletonization and cross-section regression to virtually verify the result and control the local size for additive manufacturing. is investigated in general. In this paper, a holistic design is understood as a design that considers various compliances as an objective function. This parameterization uses the automated determination of beam parameters by so-called curve skeletonization with subsequent cross-section shape parameter estimation based on moments of area, especially for multi-objective optimized shapes. An essential contribution is the linking of the parameterization with the results of the structural optimization, e.g., to include properties such as boundary conditions, load conditions, sensitivities or even density variables in the curve skeleton parameterization. The parameterization focuses on guiding the skeletonization based on the information provided by the optimization and the finite element model. In addition, the cross-section detection considers circular, elliptical, and tensor product spline cross-sections that can be applied to various shape descriptors such as convolutional surfaces, subdivision surfaces, or constructive solid geometry. The shape parameters of these cross-sections are estimated using stiffness distributions, moments of area of 2D images, and convolutional neural networks with a tailored loss function to moments of area. Each final geometry is designed by extruding the cross-section along the appropriate curve segment of the beam and joining it to other beams by using only unification operations. The focus of multi-objective structural optimization considering 1D, 2D and 3D elements is on cases that can be modeled using equations by the Poisson equation and linear elasticity. This enables the development of designs in application areas such as thermal conduction, electrostatics, magnetostatics, potential flow, linear elasticity and diffusion, which can be optimized in combination or individually. Due to the simplicity of the cases defined by the Poisson equation, no experts are required, so that many conceptual designs can be generated and reconstructed by ordinary users with little effort. Specifically for 1D elements, a element stiffness matrices for tensor product spline cross-sections are derived, which can be used to optimize a variety of lattice structures and automatically convert them into free-form surfaces. For 2D elements, non-local trigonometric interpolation functions are used, which should significantly increase interpretability of the density distribution. To further improve the optimization, a parameter-free mesh deformation is embedded so that the compliances can be further reduced by locally shifting the node positions. Finally, the proposed end-to-end optimization and parameterization is applied to verify a linear elasto-static optimization result for and to satisfy local size constraint for the manufacturing with selective laser melting of a heat transfer optimization result for a heat sink of a CPU. For the elasto-static case, the parameterization is adjusted until a certain criterion (displacement) is satisfied, while for the heat transfer case, the manufacturing constraints are satisfied by automatically changing the local size with the proposed parameterization. This heat sink is then manufactured without manual adjustment and experimentally validated to limit the temperature of a CPU to a certain level.:TABLE OF CONTENT III I LIST OF ABBREVIATIONS V II LIST OF SYMBOLS V III LIST OF FIGURES XIII IV LIST OF TABLES XVIII 1. INTRODUCTION 1 1.1 RESEARCH DESIGN AND MOTIVATION 6 1.2 RESEARCH THESES AND CHAPTER OVERVIEW 9 2. PRELIMINARIES OF TOPOLOGY OPTIMIZATION 12 2.1 MATERIAL INTERPOLATION 16 2.2 TOPOLOGY OPTIMIZATION WITH PARAMETER-FREE SHAPE OPTIMIZATION 17 2.3 MULTI-OBJECTIVE TOPOLOGY OPTIMIZATION WITH THE WEIGHTED SUM METHOD 18 3. SIMULTANEOUS SIZE, TOPOLOGY AND PARAMETER-FREE SHAPE OPTIMIZATION OF WIREFRAMES WITH B-SPLINE CROSS-SECTIONS 21 3.1 FUNDAMENTALS IN WIREFRAME OPTIMIZATION 22 3.2 SIZE AND TOPOLOGY OPTIMIZATION WITH PERIODIC B-SPLINE CROSS-SECTIONS 27 3.3 PARAMETER-FREE SHAPE OPTIMIZATION EMBEDDED IN SIZE OPTIMIZATION 32 3.4 WEIGHTED SUM SIZE AND TOPOLOGY OPTIMIZATION 36 3.5 CROSS-SECTION COMPARISON 39 4. NON-LOCAL TRIGONOMETRIC INTERPOLATION IN TOPOLOGY OPTIMIZATION 41 4.1 FUNDAMENTALS IN MATERIAL INTERPOLATIONS 43 4.2 NON-LOCAL TRIGONOMETRIC SHAPE FUNCTIONS 45 4.3 NON-LOCAL PARAMETER-FREE SHAPE OPTIMIZATION WITH TRIGONOMETRIC SHAPE FUNCTIONS 49 4.4 NON-LOCAL AND PARAMETER-FREE MULTI-OBJECTIVE TOPOLOGY OPTIMIZATION 54 5. FUNDAMENTALS IN SKELETON GUIDED SHAPE PARAMETRIZATION IN TOPOLOGY OPTIMIZATION 58 5.1 SKELETONIZATION IN TOPOLOGY OPTIMIZATION 61 5.2 CROSS-SECTION RECOGNITION FOR IMAGES 66 5.3 SUBDIVISION SURFACES 67 5.4 CONVOLUTIONAL SURFACES WITH META BALL KERNEL 71 5.5 CONSTRUCTIVE SOLID GEOMETRY 73 6. CURVE SKELETON GUIDED BEAM PARAMETRIZATION OF TOPOLOGY OPTIMIZATION RESULTS 75 6.1 FUNDAMENTALS IN SKELETON SUPPORTED RECONSTRUCTION 76 6.2 SUBDIVISION SURFACE PARAMETRIZATION WITH PERIODIC B-SPLINE CROSS-SECTIONS 78 6.3 CURVE SKELETONIZATION TAILORED TO TOPOLOGY OPTIMIZATION WITH PRE-PROCESSING 82 6.4 SURFACE RECONSTRUCTION USING LOCAL STIFFNESS DISTRIBUTION 86 7. CROSS-SECTION SHAPE PARAMETRIZATION FOR PERIODIC B-SPLINES 96 7.1 PRELIMINARIES IN B-SPLINE CONTROL GRID ESTIMATION 97 7.2 CROSS-SECTION EXTRACTION OF 2D IMAGES 101 7.3 TENSOR SPLINE PARAMETRIZATION WITH MOMENTS OF AREA 105 7.4 B-SPLINE PARAMETRIZATION WITH MOMENTS OF AREA GUIDED CONVOLUTIONAL NEURAL NETWORK 110 8. FULLY AUTOMATED COMPLIANCE OPTIMIZATION AND CURVE-SKELETON PARAMETRIZATION FOR A CPU HEAT SINK WITH SIZE CONTROL FOR SLM 115 8.1 AUTOMATED 1D THERMAL COMPLIANCE MINIMIZATION, CONSTRAINED SURFACE RECONSTRUCTION AND ADDITIVE MANUFACTURING 118 8.2 AUTOMATED 2D THERMAL COMPLIANCE MINIMIZATION, CONSTRAINT SURFACE RECONSTRUCTION AND ADDITIVE MANUFACTURING 120 8.3 USING THE HEAT SINK PROTOTYPES COOLING A CPU 123 9. CONCLUSION 127 10. OUTLOOK 131 LITERATURE 133 APPENDIX 147 A PREVIOUS STUDIES 147 B CROSS-SECTION PROPERTIES 149 C CASE STUDIES FOR THE CROSS-SECTION PARAMETRIZATION 155 D EXPERIMENTAL SETUP 15

A model-based approach to recovering the structure of a plant from images

We present a method for recovering the structure of a plant directly from a small set of widely-spaced images. Structure recovery is more complex than shape estimation, but the resulting structure estimate is more closely related to phenotype than is a 3D geometric model. The method we propose is applicable to a wide variety of plants, but is demonstrated on wheat. Wheat is made up of thin elements with few identifiable features, making it difficult to analyse using standard feature matching techniques. Our method instead analyses the structure of plants using only their silhouettes. We employ a generate-and-test method, using a database of manually modelled leaves and a model for their composition to synthesise plausible plant structures which are evaluated against the images. The method is capable of efficiently recovering accurate estimates of plant structure in a wide variety of imaging scenarios, with no manual intervention

A Cosmic Watershed: the WVF Void Detection Technique

On megaparsec scales the Universe is permeated by an intricate filigree of clusters, filaments, sheets and voids, the Cosmic Web. For the understanding of its dynamical and hierarchical history it is crucial to identify objectively its complex morphological components. One of the most characteristic aspects is that of the dominant underdense Voids, the product of a hierarchical process driven by the collapse of minor voids in addition to the merging of large ones. In this study we present an objective void finder technique which involves a minimum of assumptions about the scale, structure and shape of voids. Our void finding method, the Watershed Void Finder (WVF), is based upon the Watershed Transform, a well-known technique for the segmentation of images. Importantly, the technique has the potential to trace the existing manifestations of a void hierarchy. The basic watershed transform is augmented by a variety of correction procedures to remove spurious structure resulting from sampling noise. This study contains a detailed description of the WVF. We demonstrate how it is able to trace and identify, relatively parameter free, voids and their surrounding (filamentary and planar) boundaries. We test the technique on a set of Kinematic Voronoi models, heuristic spatial models for a cellular distribution of matter. Comparison of the WVF segmentations of low noise and high noise Voronoi models with the quantitatively known spatial characteristics of the intrinsic Voronoi tessellation shows that the size and shape of the voids are succesfully retrieved. WVF manages to even reproduce the full void size distribution function.Comment: 24 pages, 15 figures, MNRAS accepted, for full resolution, see http://www.astro.rug.nl/~weygaert/tim1publication/watershed.pd

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Shape Animation with Combined Captured and Simulated Dynamics

We present a novel volumetric animation generation framework to create new types of animations from raw 3D surface or point cloud sequence of captured real performances. The framework considers as input time incoherent 3D observations of a moving shape, and is thus particularly suitable for the output of performance capture platforms. In our system, a suitable virtual representation of the actor is built from real captures that allows seamless combination and simulation with virtual external forces and objects, in which the original captured actor can be reshaped, disassembled or reassembled from user-specified virtual physics. Instead of using the dominant surface-based geometric representation of the capture, which is less suitable for volumetric effects, our pipeline exploits Centroidal Voronoi tessellation decompositions as unified volumetric representation of the real captured actor, which we show can be used seamlessly as a building block for all processing stages, from capture and tracking to virtual physic simulation. The representation makes no human specific assumption and can be used to capture and re-simulate the actor with props or other moving scenery elements. We demonstrate the potential of this pipeline for virtual reanimation of a real captured event with various unprecedented volumetric visual effects, such as volumetric distortion, erosion, morphing, gravity pull, or collisions

Feature preserving noise removal for binary voxel volumes using 3D surface skeletons

Skeletons are well-known descriptors that capture the geometry and topology of 2D and 3D shapes. We leverage these properties by using surface skeletons to remove noise from 3D shapes. For this, we extend an existing method that removes noise, but keeps important (salient) corners for 2D shapes. Our method detects and removes large-scale, complex, and dense multiscale noise patterns that contaminate virtually the entire surface of a given 3D shape, while recovering its main (salient) edges and corners. Our method can treat any (voxelized) 3D shapes and surface-noise types, is computationally scalable, and has one easy-to-set parameter. We demonstrate the added-value of our approach by comparing our results with several known 3D shape denoising methods

Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model

Motivation: Digital reconstruction of 3D neuron structures is an important step toward reverse engineering the wiring and functions of a brain. However, despite a number of existing studies, this task is still challenging, especially when a 3D microscopic image has low single-to-noise ratio and discontinued segments of neurite patterns

Determining Alpha-Helix Correspondence for Protein Structure Prediction from Cryo-EM Density Maps, Master\u27s Thesis, May 2007

Determining protein structure is an important problem for structural biologists, which has received a significant amount of attention in the recent years. In this thesis, we describe a novel, shape-modeling approach as an intermediate step towards recovering 3D protein structures from volumetric images. The input to our method is a sequence of alpha-helices that make up a protein, and a low-resolution volumetric image of the protein where possible locations of alpha-helices have been detected. Our task is to identify the correspondence between the two sets of helices, which will shed light on how the protein folds in space. The central theme of our approach is to cast the correspondence problem as that of shape matching between the 3D volume and the 1D sequence. We model both the shapes as attributed relational graphs, and formulate a constrained inexact graph matching problem. To compute the matching, we developed an optimal algorithm based on the A*-search with several choices of heuristic functions. As demonstrated in a suite of real protein data, the shape-modeling approach is capable of correctly identifying helix correspondences in noise-abundant volumes with minimal or no user intervention

Medial Axis Approximation with Constrained Centroidal Voronoi Diagrams On Discrete Data

International audienceIn this paper, we present a novel method for me-dial axis approximation based on Constrained Centroidal Voronoi Diagram of discrete data (image, volume). The proposed approach is based on the shape boundary subsampling by a clustering approach which generates a Voronoi Diagram well suited for Medial Axis extraction. The resulting Voronoi Diagram is further filtered so as to capture the correct topology of the medial axis. The resulting medial axis appears largely invariant with respect to typical noise conditions in the discrete data. The method is tested on various synthetic as well as real images. We also show an application of the approximate medial axis to the sizing field for triangular and tetrahedral meshing