Arnaud Gelas's research while affiliated with Harvard Medical School and other places
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Publications (37)
Epithelial cells acquire functionally important shapes (e.g., squamous, cuboidal, columnar) during development. Here, we combine theory, quantitative imaging, and perturbations to analyze how tissue geometry, cell divisions, and mechanics interact to shape the presumptive enveloping layer (pre-EVL) on the zebrafish embryonic surface. We find that,...
In the last decade, level-set methods have been actively developed for applications in image registration, segmentation, tracking, and reconstruction. However, the development of a wide variety of level-set PDEs and their numerical discretization schemes, coupled with hybrid combinations of PDE terms, stopping criteria, and reinitialization strateg...
Sharply delineated domains of cell types arise in developing tissues under instruction of inductive signal (morphogen) gradients, which specify distinct cell fates at different signal levels. The translation of a morphogen gradient into discrete spatial domains relies on precise signal responses at stable cell positions. However, cells in developin...
Intensity inhomogeneities often occur in medical images, especially when using magnetic resonance imaging. In these images, the standard Chan-and-Vese levelset segmentation method may not work properly, as it assumes constant intensity distributions for foreground and background. Recently, a novel method was published that models the intensities as...
In order to test our software GoFigure2 for the visualization and the processing of extremely large 3D+t microscopy images, we utilized the visual programming technology Sikuli to automate our GUI testing. We then integrated these Sikuli tests into CTest and used CDash to report the results on a dashboard with the view to test our software automati...
The human cerebral cortex is one of the most complicated structures in the body. It has a highly convoluted structure with much of the cortical sheet buried in sulci. Based on cytoarchitectural and functional imaging studies, it is possible to segment the cerebral cortex into several subregions. While it is only possible to differentiate the true a...
This document describes a project that can compare many images simultaneously in a synchronized manner. Such an application can be used in any ITK/VTK image processing pipelines; the programmer can use it to quickly visualize and compare intermediate results of used filters within the pipeline.The goals of this project are two folds: (i) to be inte...
We propose an anisotropic diffusion method to denoise and aid the reconstruction of planar objects in three-dimensional images. The contribution of this paper is the development of a planarity function characterizing plate-like structures using an image Hessian's eigensystem. We then construct a diffusion tensor for anisotropically smoothing plates...
An Insight Toolkit (ITK) algorithm for adaptively thresholding images is presented in this paper. Cur-rently, the usage of thresholding methods in ITK has made use of global thresholds, confidence con-nected thresholds and neighborhood strategies. The current work extends these family of filters by set-ting thresholds adaptively in local image regi...
In analysis of microscopy based images, a major challenge lies in splitting apart cells that appear to overlap because they are too densely packed. This task is complicated by the physics of the image acquisition that causes large variations in pixel intensities. Each image typically contains thousands of cells with each cell having a different ori...
An Insight Toolkit (ITK) algorithm for detection of spherical objects using Hough methods with voting is presented in this paper. Currently, the usage of Hough methods for detecting linear and circular elements exists for 2D images in ITK. The current work extends those filters in several ways. Firstly, the new filters operate on N-dimensional imag...
We consider the problem of segmenting 3D images that contain a dense collection of spatially correlated objects, such as fluorescent labeled cells in tissue. Our approach involves an initial modeling phase followed by a data-fitting segmentation phase. In the first phase, cell shape (membrane bound) is modeled implicitly using a parametric distribu...
We present a high performance variant of the popular geodesic active contours which are used for splitting cell clusters in microscopy images. Previously, we implemented a linear pipelined version that incorporates as many cues as possible into developing a suitable level-set speed function so that an evolving contour exactly segments a cell/nuclei...
In this paper, we propose a new algorithm to mesh implicit surfaces which produces meshes both with a good triangle aspect ratio as well as a good approximation quality. The number of vertices of the output mesh is defined by the end-user. For this goal, we perform a two-stage processing: an initialization step followed by an iterative optimization...
During embryogenesis, cells coordinate to form geometric arrangements. These arrangements are initially noticed as stereotypical clumps of cells that further divide to form a rigorous structure with a high density of cells. In this work, we explore density-based segmentation and tracking of cellular structures as observed in microscopy images. Usin...
An Insight Toolkit (ITK) processing framework for segmenting and tracking nuclei in time-lapse microscopy images using coupled active contours is presented in this paper. We implement the method of Dufour et al.[2] to segment and track cells in fluorescence microscopy images. The basic idea is to model the image as a constant intensity background w...
An Insight Toolkit (ITK) processing framework for simultaneous segmentation of multiple objects using active contours without edges is presented in this paper. These techniques are also popularly referred to as multiphase methods. Earlier, we had an implemented the Chan and Vese [1] algorithm that uses level- sets to accomplish region segmentation...
An Insight Toolkit (ITK) processing framework for segmentation using active contours without edges is presented in this paper. Our algorithm is based on the work of Chan and Vese [1] that uses level- sets to accomplish region segmentation in images with poor or no gradient information. The basic idea is to partion the image into two piecewise const...
An Insight Toolkit (ITK) processing framework for blob segmentation with applications to microscopy images is presented in this paper. Our algorithm is a refinement of the work of Mosaliganti et al. [3] for splitting cell clusters. The basic idea is to incorporate as many cues as possible into developing a suitable level-set speed function so that...
This paper describes the implementation of a surface smoothing filter in ITK, based ont he Quad Edge Mesh surface data structure.
The increasing complexity of human body models enabled by advances in diagnostic imaging, computing, and growing knowledge calls for the development of a new generation of systems for intelligent exploration of these models. Here, we introduce a novel paradigm for the exploration of digital body models illustrating cerebral vasculature. It enables...
Computing local curvatures of a given surface is important for applications, shape analysis, surface segmentation, meshing, and surface evolution. For a given smooth surface (with a given analytical expression which is sufficiently differentiable) curvatures can be analytically and directly computed. However in real applications, one often deals wi...
We have previously developed a new surface mesh data structure in itk (~). In this document we describe a new filter () to estimate normals for a given triangular surface mesh in this data structure. Here we describe the implementation and use of this filter for calculating normals of a .
The \emph{Delaunay triangulation} is the triangulation of a set of points which maximizes the minimum angle of all angles of the triangles, and thus triangle aspect ratios. So converting a non Delaunay triangulation into a Delaunay triangulation, \emph{Delaunay conforming}, improves the all triangle aspect ratios and avoid elongated triangles. Note...
When dealing with meshes, it is often preferable to work with a lower resolution mesh for computational time purpose, display. The process of reducing a given mesh, mesh decimation, is thus an important step in most of pipeline dealing with meshes. Incremental decimation algorithms, the most popular ones, consists of iteratively removing one point...
When dealing with functional minimization, or maximization, it can sometimes be solved by a greedy algorithm. To implement greedy algorithm one needs priority queue container, i.e. get for a very low cost the lowest or highest element present in a sorted container. Whenever the priority of one element present in the queue needs to be modified, stan...
Parameterization of surfaces, sometimes alled ”‘flattening”’ as it maps a surface embedded in 3D into its intrinsic 2D domain, is a powerfull tool for the analysis of surfaces. For the past years, there has been a growing interest in the Community that even lead to one implementation of one special type of parameterization in ITK [1,5,8,9]. We are...
We present an original Radial Basis Functions-based multiphase level set approach for the segmentation of cardiac structures
in echocardiography. The method relies on two main contributions. We first describe a distribution allowing for the modeling
of the radiofrequency signal for both blood and myocardial regions. We then formulate the problem of...
This work presents an algorithm for the segmentation of myocardial regions in echocardiography imaging based on the statistics of the radiofrequency image. We formulate the problem of segmentation in a maximum likelihood framework using the Generalized Gaussian as an a priori distribution. We minimize the resulting functional using a radial basis f...
We consider a recent parametric level-set segmentation approach where the implicit interface is the zero level of a continuous function expanded onto compactly supported radial basis functions, defined by their centers, coefficients and supports. We propose to introduce prior knowledge of the shape to be recovered by placing the centers quasi-unifo...
This paper approaches the problem of volumetric mesh creation from scattered prior data for biomechanical simu-lations using the Finite Element Method. In order to cre-ate high quality meshes, we investigate the use of implicit surface reconstruction methods, together with a novel "bit-ing" meshing algorithm. The proposed method is fast, cre-ates g...
We propose a new approach for surface reconstruction from any unorganized point set, with a fixed amount of parameters. First, we consider some local approximations by compactly supported radial basis functions (CSRBFs), then blend them by a partition of unity method (PU). In our scheme, we start by selecting CSRBFs centers, then construct partitio...
We propose a novel method for reconstructing d dimensional signals with irregular samples, without any restriction on their positions. We develop a multi-resolution approximation scheme using compactly supported radial basis functions (CSRBFs). Samples are first clustered using principal component analysis and their centroids define CSRBF centers....
We propose two novel methods for reconstructing d-dimensional signals with irregular samples, without any restriction on their positions. First approach is an approximation with a fixed number of compactly supported radial basis functions (CSRBFs). Whereas the second one is a multiresolution approach with a fixed error bound, in which we only add C...
Most of the meshes coming from a variety of source are over sampled and exhibit highly irregular connectivity that prevent efficient wavelet analysis. Remeshing comes as a solution to sampling and connectivity optimization with respect to the geometry. The main drawback of existing subdivision remeshing approaches is the lack of control either on t...
We consider the construction of a multiresolution triangular mesh for 3D model-based segmentation. In the 3D Snake approach this model needs to be both uniform and regular for convergence purposes. We propose here a remeshing algorithm to compute such a model from an arbitrary triangular mesh. The input mesh is first parameterized in 2D. The output...
Citations
... (3) Area and normal calculation: The last preprocessing step is to calculate the area and the orientation of the surface normal of each triangle [20,22,23]. ...
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... Optionally, adaptive histogram equalization can be applied to enhance contrast [16]. Following this, an edge-free active contour model [17,18] is solved to segment all cells contained in the local region of interest. This model seeks to minimize the levelset energy functional, ...
... In such situations, concurrently interacting and evolving level-sets provide optimal and efficient image segmentation solutions. Multi-object methods (Dufour et al., 2005; Mosaliganti et al., 2009a,c) use a unique level-set function per anatomical structure in the image. Overlaps among the level-set functions can be penalized or encouraged through a special term placed in each of the level-set update equations. ...
... uk/). First, a rough outline of the eye was constructed on each sequence by using the 3D Hough filtering approach implemented in ITK 27 . These masks, extrapolated by a radius of 25 mm, were used as a region of interest for co-registration of the images of a specific subject. ...
... Within the contour evolution methods, two main subcategories can be distinguished: non-parametric and parametric methods. The first category encompasses classic image processing methods such as level-sets and active contours (Sethian 1999;Mosaliganti et al. 2009;Delgado-Gonzalo et al. 2012). Briefly, the contour of each object is described as a set of boundary voxels without any specific shape. ...
... Leventon stated the evolution by the following pde [12]: ...
... 3. Choose the threshold mode. TiQuant provides in most instances where thresholding is applied three different methods: "Adaptive Otsu-Threshold" [ 22 ], (global) "Otsu-Threshold" [ 23 ], and "Manual Threshold". Recommended is the use of "Adaptive Otsu-Threshold" which will yield superior results in most cases. ...
... It has been observed that epithelial cells have high rates of cell division, to allow cell remodeling and homeostasis, among other functions, due to the presence of self-renewing stem cells (Blanpain et al. 2007;Moore & Lemischka 2006) which would allow the migration of molecules and cells such as PMNs. Also, it has been widely reported that tight and adherent junctions play an important role in determining the shape, function, and polarity, as well as the regulation of the permeability of epithelia (Baum & Georgiou 2011;Tsukita et al. 2001), which also react to stimuli, modulating cell division (Xiong et al. 2014); when these junctions are separated, the permeability increases greatly, inducing the activation of the immune system in the mucosal membranes (Suzuki 2013). Likewise, when epithelial renewal occurs, the tight junctions guide the reforming of the epithelial mechanical barrier (Le Bras & Le Borgne 2014). ...
... De nombreuses méthodes de génération de maillages existent. Nous en avons notamment proposé une, basée sur une discrétisation de l'espace en grille régulière [73]. Pour toutes les expériences présentées de ce chapitre, le logiciel de maillage utilisé est GHS3D [74]. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/272182760701953-1441904835077_Q64/Remy-Prost.jpg)
![[object Object]](https://i1.rgstatic.net/ii/profile.image/272439384997903-1441966020014_Q64/Patrick-Clarysse.jpg)
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... Our strategy, in spite of being seemingly heuristic, exactly mimics the process of eliminating ownerless regions. As Figure 4 shows, our point-insertion strategy needs only 13 iterations to get a manifold mesh with 769 vertices while [14] needs 35 iterations to get a manifold mesh with 1251 vertices. In addition, we must point out that the strategy in [14] may fail for some special cases (e.g., containing thin tube parts). ...
