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

Deformable Multisurface Segmentation of the Spine for Orthopedic Surgery Planning and Simulation

Purpose: We describe a shape-aware multisurface simplex deformable model for the segmentation of healthy as well as pathological lumbar spine in medical image data. Approach: This model provides an accurate and robust segmentation scheme for the identification of intervertebral disc pathologies to enable the minimally supervised planning and patient-specific simulation of spine surgery, in a manner that combines multisurface and shape statistics-based variants of the deformable simplex model. Statistical shape variation within the dataset has been captured by application of principal component analysis and incorporated during the segmentation process to refine results. In the case where shape statistics hinder detection of the pathological region, user assistance is allowed to disable the prior shape influence during deformation. Results: Results demonstrate validation against user-assisted expert segmentation, showing excellent boundary agreement and prevention of spatial overlap between neighboring surfaces. This section also plots the characteristics of the statistical shape model, such as compactness, generalizability and specificity, as a function of the number of modes used to represent the family of shapes. Final results demonstrate a proof-of-concept deformation application based on the open-source surgery simulation Simulation Open Framework Architecture toolkit. Conclusions: To summarize, we present a deformable multisurface model that embeds a shape statistics force, with applications to surgery planning and simulation

Multiresolution Subdivision Snakes

We present a new family of snakes that satisfy the property of multiresolution by exploiting subdivision schemes. We show in a generic way how to construct such snakes based on an admissible subdivision mask. We derive the necessary energy formulations and provide the formulas for their efficient computation. Depending on the choice of the mask, such models have the ability to reproduce trigonometric or polynomial curves. They can also be designed to be interpolating, a property that is useful in user-interactive applications. We provide explicit examples of subdivision snakes and illustrate their use for the segmentation of bioimages. We show that they are robust in the presence of noise and provide a multiresolution algorithm to enlarge their basin of attraction, which decreases their dependence on initialization compared to singleresolution snakes. We show the advantages of the proposed model in terms of computation and segmentation of structures with different sizes

Image Segmentation Using Weak Shape Priors

The problem of image segmentation is known to become particularly challenging in the case of partial occlusion of the object(s) of interest, background clutter, and the presence of strong noise. To overcome this problem, the present paper introduces a novel approach segmentation through the use of "weak" shape priors. Specifically, in the proposed method, an segmenting active contour is constrained to converge to a configuration at which its geometric parameters attain their empirical probability densities closely matching the corresponding model densities that are learned based on training samples. It is shown through numerical experiments that the proposed shape modeling can be regarded as "weak" in the sense that it minimally influences the segmentation, which is allowed to be dominated by data-related forces. On the other hand, the priors provide sufficient constraints to regularize the convergence of segmentation, while requiring substantially smaller training sets to yield less biased results as compared to the case of PCA-based regularization methods. The main advantages of the proposed technique over some existing alternatives is demonstrated in a series of experiments.Comment: 27 pages, 8 figure

B-Spline Snakes: A Flexible Tool for Parametric Contour Detection

We present a novel formulation for B-spline snakes that can be used as a tool for fast and intuitive contour outlining. We start with a theoretical argument in favor of splines in the traditional formulation by showing that the optimal, curvature-constrained snake is a cubic spline, irrespective of the form of the external energy field. Unfortunately, such regularized snakes suffer from slow convergence speed because of a large number of control points, as well as from difficulties in determining the weight factors associated to the internal energies of the curve. We therefore propose an alternative formulation in which the intrinsic scale of the spline model is adjusted a priori; this leads to a reduction of the number of parameters to be optimized and eliminates the need for internal energies (i.e., the regularization term). In other words, we are now controlling the elasticity of the spline implicitly and rather intuitively by varying the spacing between the spline knots. The theory is embedded into a multi-resolution formulation demonstrating improved stability in noisy image environments. Validation results are presented, comparing the traditional snake using internal energies and the proposed approach without internal energies, showing the similar performance of the latter. Several biomedical examples of applications are included to illustrate the versatility of the method

Composition-guided image acquisition

textTo make a picture more appealing, professional photographers apply a wealth of photographic composition rules, of which amateur photographers are of- ten unaware. This dissertation aims at providing in-camera feedback to the amateur photographer while taking pictures. The proposed algorithms do not depend on prior knowledge of the indoor/outdoor setting or scene, and are amenable to software implementation on fixed-point programmable digital signal processors available in digital still cameras. The key enabling step in automating photographic composition rules is to locate the main subject. Digital still image acquisition maps the 3-D world onto a 2-D picture. By using the 2-D picture alone, segmenting the main subject without prior knowledge of the scene is ill-posed. Even with prior knowledge, segmentation is often computationally intensive and error prone. This dissertation defends the idea that reliable main subject segmenta- tion without prior knowledge of scene and setting may be achieved by acquiring a single picture, in which the optical system blurs objects not in the plane of focus. After segmentation, photographic composition rules may be automated. In this context, segmentation only needs to approximately and not precisely locate the main subject. In this dissertation, I combine optical and digital image processing to perform the segmentation of the main subject without prior knowledge of the scene. In particular, I propose to acquire a picture in which the main subject is in focus, and the shutter aperture is fully open. The lens optics will blur any object not in the plane of focus. For the acquired picture, I develop a computationally simple one-pass algorithm to segment the main subject. The post segmentation objective is to automate selected photographic composition rules. The algorithms can either be applied on the picture taken with the objects not in the plane of focus blurred, or on a user-intended picture with the same focal length settings. This way, in-camera feedback can be provided to the amateur photographer, in the form of alternate compositions of the same scene. I automate three photographic composition rules: (1) placement of the main subject obeying the rule-of-thirds, (2) background blurring to simulate the main subject being in motion or decrease the depth-of-field of the picture, and (3) merger detection and mitigation when equally focused main subject and background objects merge as one object. The primary contributions of the dissertation are in digital still image processing. The first is the automation of segmentation of the main subject in a single still picture assisted by optical pre-processing. The second is the automation of main subject placement, artistic background blur, and merger detection and mitigation to try to improve photographic composition.Electrical and Computer Engineerin