scholarly journals The complex three-dimensional organization of epithelial tissues

Development ◽  
2021 ◽  
Vol 148 (1) ◽  
pp. dev195669
Author(s):  
Pedro Gómez-Gálvez ◽  
Pablo Vicente-Munuera ◽  
Samira Anbari ◽  
Javier Buceta ◽  
Luis M. Escudero
Keyword(s):  
Three Dimensional ◽  
Complex Problem ◽  
Three Dimensions ◽  
Cellular Organization ◽  
Dimensional Representation ◽  
Epithelial Tissues ◽  
Tissue Organization ◽  
Realistic Approach ◽  
Organization Problem ◽  
Cell Shapes

ABSTRACTUnderstanding the cellular organization of tissues is key to developmental biology. In order to deal with this complex problem, researchers have taken advantage of reductionist approaches to reveal fundamental morphogenetic mechanisms and quantitative laws. For epithelia, their two-dimensional representation as polygonal tessellations has proved successful for understanding tissue organization. Yet, epithelial tissues bend and fold to shape organs in three dimensions. In this context, epithelial cells are too often simplified as prismatic blocks with a limited plasticity. However, there is increasing evidence that a realistic approach, even from a reductionist perspective, must include apico-basal intercalations (i.e. scutoidal cell shapes) for explaining epithelial organization convincingly. Here, we present an historical perspective about the tissue organization problem. Specifically, we analyze past and recent breakthroughs, and discuss how and why simplified, but realistic, in silico models require scutoidal features to address key morphogenetic events.

scholarly journals Geometric constraints alter cell arrangements within curved epithelial tissues

2017 ◽  
Vol 28 (25) ◽  
pp. 3582-3594 ◽  
Author(s):  
Jean-Francois Rupprecht ◽  
Kok Haur Ong ◽  
Jianmin Yin ◽  
Anqi Huang ◽  
Huy-Hong-Quan Dinh ◽  
...  
Keyword(s):  
Cell Morphology ◽  
Three Dimensional ◽  
Quantitative Information ◽  
Geometric Constraints ◽  
Three Dimensions ◽  
Drosophila Embryo ◽  
Anterior Pole ◽  
Epithelial Tissues ◽  
Early Drosophila Embryo

Organ and tissue formation are complex three-dimensional processes involving cell division, growth, migration, and rearrangement, all of which occur within physically constrained regions. However, analyzing such processes in three dimensions in vivo is challenging. Here, we focus on the process of cellularization in the anterior pole of the early Drosophila embryo to explore how cells compete for space under geometric constraints. Using microfluidics combined with fluorescence microscopy, we extract quantitative information on the three-dimensional epithelial cell morphology. We observed a cellular membrane rearrangement in which cells exchange neighbors along the apical-basal axis. Such apical-to-basal neighbor exchanges were observed more frequently in the anterior pole than in the embryo trunk. Furthermore, cells within the anterior pole skewed toward the trunk along their long axis relative to the embryo surface, with maximum skew on the ventral side. We constructed a vertex model for cells in a curved environment. We could reproduce the observed cellular skew in both wild-type embryos and embryos with distorted morphology. Further, such modeling showed that cell rearrangements were more likely in ellipsoidal, compared with cylindrical, geometry. Overall, we demonstrate that geometric constraints can influence three-dimensional cell morphology and packing within epithelial tissues.

scholarly journals 2.5D Visualisation of Overlapping Biological Networks

2008 ◽  
Vol 5 (1) ◽  
pp. 77-93 ◽  
Author(s):  
David C.Y. Fung ◽  
Seok-Hee Hong ◽  
Dirk Koschützki ◽  
Falk Schreiber ◽  
Kai Xu
Keyword(s):  
Biological Networks ◽  
Metabolic Networks ◽  
Visual Analysis ◽  
Three Dimensional ◽  
Biological Data ◽  
Three Dimensions ◽  
Two Dimensional ◽  
Dimensional Representation ◽  
Three Dimensional Representation ◽  
Interconnected Networks

Abstract Biological data is often structured in the form of complex interconnected networks such as protein interaction and metabolic networks. In this paper, we investigate a new problem of visualising such overlapping biological networks. Two networks overlap if they share some nodes and edges. We present an approach for constructing visualisations of two overlapping networks, based on a restricted three dimensional representation. More specifically, we use three parallel two dimensional planes placed in three dimensions to represent overlapping networks: one for each network (the top and the bottom planes) and one for the overlapping part (in the middle plane).Our method aims to achieve both drawing aesthetics (or conventions) for each individual network, and highlighting the intersection part by them. Using three biological datasets, we evaluate our visualisation design with the aim to test whether overlapping networks can support the visual analysis of heterogeneous and yet interconnected networks.

Multimedia technology-assisted stereo geometry teaching

2021 ◽  
pp. 002072092098468
Author(s):  
Yu Wang
Keyword(s):  
Three Dimensional ◽  
Three Dimensions ◽  
Multimedia Technology ◽  
Traditional Teaching ◽  
Dimensional Representation ◽  
Three Dimensional Representation ◽  
Education Community ◽  
The Media ◽  
Network Platform ◽  
Control Interaction

Multimedia technology makes our life more stereoscopic and intuitive. Graphic images and animations are the most important part of multimedia information expression. It makes our visual effects of three-dimensional representation of things more vivid, like the plane and three-dimensional we usually see. As with the picture, modern multimedia technology transforms our lives into three dimensions, integration, control, interaction and interaction. For the vivid three-dimensional representation of three-dimensional geometric figures in teaching, not only is it limited to the geometric composition of a piece of chalk, but more with the wide application of multimedia technology, multimedia-assisted teaching, especially multimedia-assisted three-dimensional geometric figure teaching is playing more and more The important role, through the aid of multimedia, has cultivated students’ spatial abstract thinking ability and ability to understand graphics and theorems. As multimedia becomes more and more concerned by the education community, this paper is about the question of why multimedia technology should be used to assist the teaching and application of solid geometry applications, and how to apply multimedia technology to achieve the maximum value of the teaching effect of stereo geometry. A lot of experimental research has been carried out. Through experiments, we have built a more complete multimedia assistant teaching system, which is beneficial for students to acquire new knowledge on the Internet. The multimedia technology-assisted three-dimensional geometric method is more conducive to mobilizing the enthusiasm and initiative of students than the traditional method. The biggest innovation of this paper is to use the indispensable advantages of traditional teaching to discount the media to the network platform. To some extent, the research in this paper enhances the guiding significance of interactive research to the actual development work.

scholarly journals Highly multiplexed molecular and cellular mapping of breast cancer tissue in three dimensions using mass tomography

2020 ◽  
Author(s):  
Raúl Catena ◽  
Alaz Özcan ◽  
Laura Kütt ◽  
Alex Plüss ◽  
Peter Schraml ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Cellular Heterogeneity ◽  
Cancer Tissue ◽  
Tissue Architecture ◽  
Tissue Microenvironment ◽  
Tissue Organization ◽  
Holistic Understanding ◽  
Cancer Sample

ABSTRACTA holistic understanding of tissue and organ structures and their functions requires the detection of molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) makes possible the detection of up to 40 antigens and specific nucleic acids simultaneously using metal-tagged antibodies or nucleic acid probes, respectively, but has so far been restricted to two-dimensional imaging. To enable use of IMC for 3D tissue analyses, we developed mass tomography, which combines quasi deformation-free serial sectioning with novel computational methods. We utilized mass tomography to analyze a breast cancer sample. The resulting 3D representation reveals spatial and cellular heterogeneity, preferential cell-to-cell interactions, detailed tissue-architecture motifs, and the unique microenvironment of a micro-invasion, where micro-metastases clonality is examined, showing that cells arising from the same invasive area, displaying very distinct phenotypes, are all able to produce initial invasive lesions. Mass tomography will provide invaluable insights into the tissue microenvironment, cellular neighborhoods, and tissue organization.

scholarly journals A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Hernán Morales-Navarrete ◽  
Fabián Segovia-Miranda ◽  
Piotr Klukowski ◽  
Kirstin Meyer ◽  
Hidenori Nonaka ◽  
...  
Keyword(s):  
Liver Tissue ◽  
Multiple Scales ◽  
Three Dimensional ◽  
Kidney Tissue ◽  
Cell Types ◽  
Tissue Architecture ◽  
High Throughput Analysis ◽  
Multi Scale ◽  
Tissue Organization ◽  
Cell Shapes

A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness.

Reconstruction of Objects from their Projections Using Orthogonal Functions

1973 ◽  
Vol 31 ◽  
pp. 268-269
Author(s):  
Elrnar Zeitler
Keyword(s):  
Unit Area ◽  
Three Dimensional ◽  
One Dimension ◽  
Spatial Density ◽  
Dimensional Representation ◽  
Orthogonal Functions ◽  
Object A ◽  
Plane Normal ◽  
Dimensional Object ◽  
Spatial Density Distribution

Considering any finite three-dimensional object, a “projection” is here defined as a two-dimensional representation of the object's mass per unit area on a plane normal to a given projection axis, here taken as they-axis. Since the object can be seen as being built from parallel, thin slices, the relation between object structure and its projection can be reduced by one dimension. It is assumed that an electron microscope equipped with a tilting stage records the projectionWhere the object has a spatial density distribution p(r,ϕ) within a limiting radius taken to be unity, and the stage is tilted by an angle 9 with respect to the x-axis of the recording plane.

Revealing gross three-dimensional structure in the SEM

1987 ◽  
Vol 45 ◽  
pp. 656-657
Author(s):  
Sterling P. Newberry
Keyword(s):  
Freeze Drying ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Small Object ◽  
Final Solution ◽  
Dimensional Representation ◽  
X Ray ◽  
Three Dimensional Representation ◽  
Freeze Dried ◽  
Critical Point Drying

The beautiful three dimensional representation of small object surfaces by the SEM leads one to search for ways to open up the sample and look inside. Could this be the answer to a better microscopy for gross biological 3-D structure? We know from X-Ray microscope images that Freeze Drying and Critical Point Drying give promise of adequately preserving gross structure. Can we slice such preparations open for SEM inspection? In general these preparations crush more readily than they slice. Russell and Dagihlian got around the problem by “deembedding” a section before imaging. This some what defeats the advantages of direct dry preparation, thus we are reluctant to accept it as the final solution to our problem. Alternatively, consider fig 1 wherein a freeze dried onion root has a window cut in its surface by a micromanipulator during observation in the SEM.

convergent-beam diffraction from surfaces

1987 ◽  
Vol 45 ◽  
pp. 30-33
Author(s):  
J. A. Eades ◽  
A. E. Smith ◽  
D. F. Lynch
Keyword(s):  
Reciprocal Lattice ◽  
Three Dimensional ◽  
Grazing Incidence ◽  
Three Dimensions ◽  
Plane Figure ◽  
Transmission Electron ◽  
Convergent Beam ◽  
Beam Patterns ◽  
Beam Diffraction

It is quite simple (in the transmission electron microscope) to obtain convergent-beam patterns from the surface of a bulk crystal. The beam is focussed onto the surface at near grazing incidence (figure 1) and if the surface is flat the appropriate pattern is obtained in the diffraction plane (figure 2). Such patterns are potentially valuable for the characterization of surfaces just as normal convergent-beam patterns are valuable for the characterization of crystals.There are, however, several important ways in which reflection diffraction from surfaces differs from the more familiar electron diffraction in transmission.GeometryIn reflection diffraction, because of the surface, it is not possible to describe the specimen as periodic in three dimensions, nor is it possible to associate diffraction with a conventional three-dimensional reciprocal lattice.

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.

Going Beyond 3-D Imaging: Automated 3-D Montaged image Analysis of Cytological Specimens

1996 ◽  
Vol 54 ◽  
pp. 282-283
Author(s):  
Badrinath Roysam ◽  
Hakan Ancin ◽  
Douglas E. Becker ◽  
Robert W. Mackin ◽  
Matthew M. Chestnut ◽  
...  
Keyword(s):  
Image Analysis ◽  
Structural Changes ◽  
Sampling Methods ◽  
Spatial Clustering ◽  
Three Dimensional ◽  
Field Of View ◽  
Cell Counting ◽  
Depth Of Field ◽  
Tissue Cell ◽  
Tissue Organization

This paper summarizes recent advances made by this group in the automated three-dimensional (3-D) image analysis of cytological specimens that are much thicker than the depth of field, and much wider than the field of view of the microscope. The imaging of thick samples is motivated by the need to sample large volumes of tissue rapidly, make more accurate measurements than possible with 2-D sampling, and also to perform analysis in a manner that preserves the relative locations and 3-D structures of the cells. The motivation to study specimens much wider than the field of view arises when measurements and insights at the tissue, rather than the cell level are needed.The term “analysis” indicates a activities ranging from cell counting, neuron tracing, cell morphometry, measurement of tracers, through characterization of large populations of cells with regard to higher-level tissue organization by detecting patterns such as 3-D spatial clustering, the presence of subpopulations, and their relationships to each other. Of even more interest are changes in these parameters as a function of development, and as a reaction to external stimuli. There is a widespread need to measure structural changes in tissue caused by toxins, physiologic states, biochemicals, aging, development, and electrochemical or physical stimuli. These agents could affect the number of cells per unit volume of tissue, cell volume and shape, and cause structural changes in individual cells, inter-connections, or subtle changes in higher-level tissue architecture. It is important to process large intact volumes of tissue to achieve adequate sampling and sensitivity to subtle changes. It is desirable to perform such studies rapidly, with utmost automation, and at minimal cost. Automated 3-D image analysis methods offer unique advantages and opportunities, without making simplifying assumptions of tissue uniformity, unlike random sampling methods such as stereology.12 Although stereological methods are known to be statistically unbiased, they may not be statistically efficient. Another disadvantage of sampling methods is the lack of full visual confirmation - an attractive feature of image analysis based methods.

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