Contact Detection Between Convex Superquadric Surfaces

Portal, Ricardo; Dias, João P.; Sousa, Leonel

doi:10.2478/v10180-010-0009-8

Cited by 20 publications

(7 citation statements)

References 7 publications

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“…To generate the synthetic data, we modeled bacterial cells as 3D rod-shaped objects comprised of individual voxels with an xy pixel size and z step interval of 130 nm × 130 nm × 130 nm, the parameters of our microscope and camera setup. 23 The 3D objects were then convolved with the point-spread function to better represent the 3D image of the bacteria. Several synthetic bacteria were randomly placed in 3D space with certain interbacterial space to make synthetic images with certain crowdedness such that cells can touch but cannot intersect (Figure 4b).…”

Section: ■ Methods Validation With Synthetic Datamentioning

confidence: 98%

“…To validate Seg-3D, we first tested it on synthetic data (Figure ). To generate the synthetic data, we modeled bacterial cells as 3D rod-shaped objects comprised of individual voxels with an xy pixel size and z step interval of 130 nm × 130 nm × 130 nm, the parameters of our microscope and camera setup . The 3D objects were then convolved with the point-spread function to better represent the 3D image of the bacteria.…”

Section: Methods Validation With Synthetic Datamentioning

confidence: 99%

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An Automated Image Analysis Method for Segmenting Fluorescent Bacteria in Three Dimensions

et al. 2017

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Single-cell fluorescence imaging is a powerful technique for studying inherently heterogeneous biological processes. To correlate a genotype or phenotype to a specific cell, images containing a population of cells must first be properly segmented. However, a proper segmentation with minimal user input becomes challenging when cells are clustered or overlapping in three dimensions. We introduce a new analysis package, Seg-3D, for the segmentation of bacterial cells in three-dimensional (3D) images, based on local thresholding, shape analysis, concavity-based cluster splitting, and morphology-based 3D reconstruction. The reconstructed cell volumes allow us to directly quantify the fluorescent signals from biomolecules of interest within individual cells. We demonstrate the application of this analysis package in 3D segmentation of individual bacterial pathogens invading host cells. We believe Seg-3D can be an efficient and simple program that can be used to analyze a wide variety of single-cell images, especially for biological systems involving random 3D orientation and clustering behavior, such as bacterial infection or colonization.

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Section: ■ Methods Validation With Synthetic Datamentioning

confidence: 98%

Section: Methods Validation With Synthetic Datamentioning

confidence: 99%

An Automated Image Analysis Method for Segmenting Fluorescent Bacteria in Three Dimensions

et al. 2017

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“…More recently, Studer et al [41] extended the modern time stepping algorithms to include a step size adjustment and extrapolation for contact detection in non-smooth dynamics. Portal et al [42] presented a methodology for contact detection between convex quadric surfaces using its implicit equations. This methodology was implemented in a multibody dynamics code in order to simulate the interpenetration between mechanical systems, particularly, the simulation of collisions with automotive vehicles and other road users, such as cars, motorcycles and pedestrians.…”

Section: Introductionmentioning

confidence: 99%

On the contact detection for contact-impact analysis in multibody systems

2010

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One of the most important and complex parts of the simulation of multibody systems with contactimpact involves the detection of the precise instant of impact. In general, the periods of contact are very small and, therefore, the selection of the time step for the integration of the time derivatives of the state variables plays a crucial role in the dynamics of multibody systems. The conservative approach is to use very small time steps throughout the analysis. However, this solution is not efficient from the computational view point. When variable time step integration algorithms are used and the pre-impact dynamics does not involve high-frequencies the integration algorithms may use larger time steps and the contact between two surfaces may start with initial penetrations that are artificially high. This fact leads either to a stall of the integration algorithm or to contact forces that are physically impossible which, in turn, lead to post-impact dynamics that is unrelated to the physical problem. The main purpose of this work is to present a general and comprehensive approach to automatically adjust the time step, in variable time step integration algorithms, in the vicinity of contact of multibody systems.The proposed methodology ensures that for any impact in a multibody system the time step of the integration is such that any initial penetration is below any prescribed threshold. In the case of the start of contact, and after a time step is complete, the numerical error control of the selected integration algorithm is forced to handle the physical criteria to accept/reject time steps in equal terms with the numerical error control that it normally uses. The main features of this approach are the simplicity of its computational implementation, its good computational efficiency and its ability to deal with the transitions between non contact and contact situations in multibody dynamics. A demonstration case provides the results that support the discussion and show the validity of the proposed methodology.

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“…Entretanto, um dos principais desafios em se utilizar este tipo de partícula em simulações com o MED está em descrever formulações matemática que permitam montar algoritmos eficientes para detecção do contato inter-partículas. Este tema tem sido estudado por diversos autores conforme pode ser visto em [10], [11], [28], [35], [36], [37] e [38]. Em todos estes trabalhos, os autores relatam que o tempo gasto na detecção do contato representa a maior parte do tempo total da simulação.…”

Section: Transformação De Cayleyunclassified

“…Considerando que a densidade do material da partícula, , é constante em todo elemento discreto, a massa de um superelipsóide dada pela equação (35).…”

Section: Transformação De Cayleyunclassified

O método dos elementos discretos com superelipsoides usando a parametrização das rotações de Rodrigues.

Sampaio¹

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Meus sinceros agradecimentos ao Prof. Paulo Pimenta, pela competente orientação, dedicação e incessante incentivo à pesquisa. À minha esposa Hellen, pelo imenso apoio durante todo doutorado, por me ajudar em todos os momentos difíceis desta etapa, e pelas grandes alegrias compartilhadas. Agradeço ao Prof. Peter Wriggers, por ter me aceitado na Leibniz Universität Hannover, para passar cinco meses sob sua coorientação, no IKM (Institut für Kontinuumsmechanik). Aos meus pais, Fernando e Eládia, e irmãos, Marco Túlio e Fernando, pelos exemplos de vida e carinho incondicional que me fortalecem todos os dias. Ao Prof. Noronha, um grande mestre e amigo, pelos conselhos sinceros e pelos incentivos para que eu me torne um Professor.

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Contact Detection Between Convex Superquadric Surfaces

Cited by 20 publications

References 7 publications

An Automated Image Analysis Method for Segmenting Fluorescent Bacteria in Three Dimensions

An Automated Image Analysis Method for Segmenting Fluorescent Bacteria in Three Dimensions

On the contact detection for contact-impact analysis in multibody systems

O método dos elementos discretos com superelipsoides usando a parametrização das rotações de Rodrigues.

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