scholarly journals Evolutionary 3D Image Segmentation of Curve Epithelial Tissues of Drosophila melanogaster

2021 ◽  
Vol 11 (14) ◽  
pp. 6410
Author(s):  
Carlos Capitán-Agudo ◽  
Beatriz Pontes ◽  
Pedro Gómez-Gálvez ◽  
Pablo Vicente-Munuera
Keyword(s):  
Drosophila Melanogaster ◽  
Evolutionary Algorithm ◽  
Three Dimensional ◽  
Fine Tuning ◽  
Contour Method ◽  
Good Convergence ◽  
Biological Images ◽  
Epithelial Tissues ◽  
Segmented Images ◽  
Confocal Images

Analysing biological images coming from the microscope is challenging; not only is it complex to acquire the images, but also the three-dimensional shapes found on them. Thus, using automatic approaches that could learn and embrace that variance would be highly interesting for the field. Here, we use an evolutionary algorithm to obtain the 3D cell shape of curve epithelial tissues. Our approach is based on the application of a 3D segmentation algorithm called LimeSeg, which is a segmentation software that uses a particle-based active contour method. This program needs the fine-tuning of some hyperparameters that could present a long number of combinations, with the selection of the best parametrisation being highly time-consuming. Our evolutionary algorithm automatically selects the best possible parametrisation with which it can perform an accurate and non-supervised segmentation of 3D curved epithelial tissues. This way, we combine the segmentation potential of LimeSeg and optimise the parameters selection by adding automatisation. This methodology has been applied to three datasets of confocal images from Drosophila melanogaster, where a good convergence has been observed in the evaluation of the solutions. Our experimental results confirm the proper performing of the algorithm, whose segmented images have been compared to those manually obtained for the same tissues.

Three-dimensional image analysis and visualization in confocal light microscopy

1993 ◽  
Vol 51 ◽  
pp. 158-159
Author(s):  
J. K. Samarabandu ◽  
R. Acharya ◽  
D. R. Pareddy ◽  
P. C. Cheng
Keyword(s):  
Depth Perception ◽  
Computer Graphic ◽  
Three Dimensional ◽  
Cellular Organization ◽  
Data Set ◽  
Computational Burden ◽  
Interactive Operation ◽  
Cell Organization ◽  
Confocal Images ◽  
3D Digitization

In the study of cell organization in a maize meristem, direct viewing of confocal optical sections in 3D (by means of 3D projection of the volumetric data set, Figure 1) becomes very difficult and confusing because of the large number of nucleus involved. Numerical description of the cellular organization (e.g. position, size and orientation of each structure) and computer graphic presentation are some of the solutions to effectively study the structure of such a complex system. An attempt at data-reduction by means of manually contouring cell nucleus in 3D was reported (Summers et al., 1990). Apart from being labour intensive, this 3D digitization technique suffers from the inaccuracies of manual 3D tracing related to the depth perception of the operator. However, it does demonstrate that reducing stack of confocal images to a 3D graphic representation helps to visualize and analyze complex tissues (Figure 2). This procedure also significantly reduce computational burden in an interactive operation.

Thermohydrodynamic Behavior of a Slider Pocket Bearing

2005 ◽  
Vol 128 (2) ◽  
pp. 312-318 ◽  
Author(s):  
Mihai B. Dobrica ◽  
Michel Fillon
Keyword(s):  
Pressure Distribution ◽  
Reverse Flow ◽  
Three Dimensional ◽  
Convective Boundary ◽  
Inertia Effects ◽  
Good Convergence ◽  
Bearing Design ◽  
The One ◽  
Volume Method ◽  
Generalized Reynolds Equation

Pocket-pads or steps are often used in journal bearing design, allowing improvement of the latter’s dynamic behavior. Similar “discontinuous” geometries are used in designing thrust bearing pads. A literature review shows that, to date, only isoviscous and adiabatic studies of such geometries have been performed. The present paper addresses this gap, proposing a complete thermohydrodynamic (THD) steady model, adapted to three-dimensional (3D) discontinuous geometries. The model is applied to the well-known geometry of a slider pocket bearing, operating with an incompressible viscous lubricant. A model based on the generalized Reynolds equation, with concentrated inertia effects, is used to determine the 2D pressure distribution. On this basis, a 3D field of velocities is constructed which, in turn, allows the resolution of the 3D energy equation. Using a variable-size grid improves the accuracy in the discontinuity region, allowing an evaluation of the magnitude of error induced by Reynolds assumptions. The equations are solved using the finite volume method. This ensures good convergence even when a significant reverse flow is present. Heat evacuation through the pad is taken into account by solving the Laplace equation with convective boundary conditions that are realistic. The runner’s temperature, assumed constant, is determined by imposing a zero value for the global heat flux balance. The constructed model gives the pressure distribution and velocity fields in the fluid, as well as the temperature distribution across the fluid and solid pad. Results show important transversal temperature gradients in the fluid, especially in the areas of minimal film thickness. This further justifies the use of a complete THD model such as the one employed.

The Boundary Contour Method for Three-Dimensional Linear Elasticity

1996 ◽  
Vol 63 (2) ◽  
pp. 278-286 ◽  
Author(s):  
A. Nagarajan ◽  
S. Mukherjee ◽  
E. Lutz
Keyword(s):  
Boundary Element Method ◽  
Boundary Element ◽  
Linear Elasticity ◽  
Three Dimensional ◽  
Contour Method ◽  
Boundary Contour ◽  
Boundary Contour Method ◽  
Novel Variant ◽  
Elasticity Problems ◽  
Element Method

This paper presents a novel variant of the boundary element method, here called the boundary contour method, applied to three-dimensional problems of linear elasticity. In this work, the surface integrals on boundary elements of the usual boundary element method are transformed, through an application of Stokes’ theorem, into line integrals on the bounding contours of these elements. Thus, in this formulation, only line integrals have to be numerically evaluated for three-dimensional elasticity problems—even for curved surface elements of arbitrary shape. Numerical results are presented for some three-dimensional problems, and these are compared against analytical solutions.

scholarly journals Three-dimensional organization of Drosophila melanogaster interphase nuclei. I. Tissue-specific aspects of polytene nuclear architecture.

1987 ◽  
Vol 104 (6) ◽  
pp. 1455-1470 ◽  
Author(s):  
M Hochstrasser ◽  
J W Sedat
Keyword(s):  
Drosophila Melanogaster ◽  
Three Dimensional ◽  
Nuclear Architecture ◽  
Close Packing ◽  
Prothoracic Gland ◽  
Cell Type ◽  
Interphase Chromosome ◽  
Tissue Specific ◽  
Spatial Domains ◽  
Four Levels

Interphase chromosome organization in four different Drosophila melanogaster tissues, covering three to four levels of polyteny, has been analyzed. The results are based primarily on three-dimensional reconstructions from unfixed tissues using a computer-based data collection and modeling system. A characteristic organization of chromosomes in each cell type is observed, independent of polyteny, with some packing motifs common to several or all tissues and others tissue-specific. All chromosomes display a right-handed coiling chirality, despite large differences in size and degree of coiling. Conversely, in each cell type, the heterochromatic centromeric regions have a unique structure, tendency to associate, and intranuclear location. The organization of condensed nucleolar chromatin is also tissue-specific. The tightly coiled prothoracic gland chromosomes are arrayed in a similar fashion to the much larger salivary gland chromosomes described previously, having polarized orientations, nonintertwined spatial domains, and close packing of the arms of each autosome, whereas hindgut and especially the unusually straight midgut chromosomes display striking departures from these regularities. Surprisingly, gut chromosomes often appear to be broken in the centric heterochromatin. Severe deformations of midgut nuclei observed during gut contractions in living larvae may account for their unusual properties. Finally, morphometric measurements of chromosome and nuclear dimensions provide insights into chromosome growth and substructure and also suggest an unexpected parallel with diploid chromatin organization.

Entrainment and Transport in Idealized Three-Dimensional Gravity Current Simulation

2006 ◽  
Vol 23 (9) ◽  
pp. 1249-1269 ◽  
Author(s):  
Yu-Heng Tseng ◽  
David E. Dietrich
Keyword(s):  
Gravity Current ◽  
Vertical Mixing ◽  
Three Dimensional ◽  
Ocean Model ◽  
Numerical Dissipation ◽  
Good Convergence ◽  
Low Viscosity ◽  
Denmark Strait ◽  
Dimensional Gravity ◽  
Fine Resolution

Abstract A purely z-coordinate Dietrich/Center for Air Sea Technology (DieCAST) ocean model is applied to the Dynamics of Overflow Mixing and Entrainment (DOME) idealized bottom density current problem that is patterned after the Denmark Strait. The numerical results show that the background viscosity plays a more important role than the chosen coordinate system in the entrainment and mixing if the background viscosity is not small enough. Both higher horizontal viscosity and coarser resolution leads to slower along-slope propagation. Reducing vertical mixing parameterization also leads to slower along-slope propagation with thicker plume size vertically. The simulation gives consistent results for the moderate- and fine-resolution runs. At a very coarse grid the dense water descends more slowly and is mainly dominated by diffusion. Time-averaged downstream transport and entrainment are not very sensitive to viscosity after the flow reaches its quasi-steady status. However, more realistic eddies and flow structures are found in low-viscosity runs. The results show good convergence of the resolved flow as expected and clarify the effects of numerical dissipation/mixing on overflow modeling. Larger numerical dissipation is not required nor recommended in z-coordinate models.

scholarly journals Mimicking Epithelial Tissues in Three-Dimensional Cell Culture Models

2018 ◽  
Vol 6 ◽  
Author(s):  
Núria Torras ◽  
María García-Díaz ◽  
Vanesa Fernández-Majada ◽  
Elena Martínez
Keyword(s):  
Cell Culture ◽  
Three Dimensional ◽  
Epithelial Tissues ◽  
Culture Models ◽  
Cell Culture Models ◽  
Dimensional Cell

A Novel Boundary Element Method for Linear Elasticity With No Numerical Integration for Two-Dimensional and Line Integrals for Three-Dimensional Problems

1994 ◽  
Vol 61 (2) ◽  
pp. 264-269 ◽  
Author(s):  
A. Nagarajan ◽  
E. Lutz ◽  
S. Mukherjee
Keyword(s):  
Boundary Element Method ◽  
Boundary Element ◽  
Numerical Integration ◽  
Linear Elasticity ◽  
Three Dimensional ◽  
Contour Method ◽  
Surface Boundary ◽  
Two Dimensional ◽  
Boundary Contour Method ◽  
Element Method

This paper presents a novel application of the boundary element method to solve problems in linear elasticity. The new method is called the Boundary Contour Method. This approach requires no numerical integration at all for two-dimensional problems and numerical evaluation of line integrals only for three-dimensional problems; even for curved line or surface boundary elements of arbitrary shape! Numerical results are presented for some two-dimensional problems.

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