scholarly journals Robust cell tracking in epithelial tissues through identification of maximum common subgraphs

2016 ◽  
Author(s):  
Jochen Kursawe ◽  
Rémi Bardenet ◽  
Jeremiah J. Zartman ◽  
Ruth E. Baker ◽  
Alexander G. Fletcher
Keyword(s):  
Cell Tracking ◽  
Positional Information ◽  
Large Cell ◽  
Field Of View ◽  
Maximum Common Subgraph ◽  
Graph Theoretic ◽  
Epithelial Tissues ◽  
Theoretic Concept ◽  
Tissue Size ◽  
Epithelial Sheets

AbstractTracking of cells in live-imaging microscopy videos of epithelial sheets is a powerful tool for investigating fundamental processes in embryonic development. Characterising cell growth, proliferation, intercalation and apoptosis in epithelia helps us to understand how morphogenetic processes such as tissue invagination and extension are locally regulated and controlled. Accurate cell tracking requires correctly resolving cells entering or leaving the field of view between frames, cell neighbour exchanges, cell removals and cell divisions. However, current tracking methods for epithelial sheets are not robust to large morphogenetic deformations and require significant manual interventions. Here, we present a novel algorithm for epithelial cell tracking, exploiting the graph-theoretic concept of a ‘maximum common subgraph’ to track cells between frames of a video. Our algorithm does not require the adjustment of tissue-specific parameters, and scales in sub-quadratic time with tissue size. It does not rely on precise positional information, permitting large cell movements between frames and enabling tracking in datasets acquired at low temporal resolution due to experimental constraints such as photoxicity. To demonstrate the method, we perform tracking on the Drosophila embryonic epidermis and compare cell-cell rearrangements to previous studies in other tissues. Our implementation is open source and generally applicable to epithelial tissues.

scholarly journals Robust cell tracking in epithelial tissues through identification of maximum common subgraphs

2016 ◽  
Vol 13 (124) ◽  
pp. 20160725 ◽  
Author(s):  
Jochen Kursawe ◽  
Rémi Bardenet ◽  
Jeremiah J. Zartman ◽  
Ruth E. Baker ◽  
Alexander G. Fletcher
Keyword(s):  
Cell Tracking ◽  
Positional Information ◽  
Large Cell ◽  
Field Of View ◽  
Maximum Common Subgraph ◽  
Graph Theoretic ◽  
Epithelial Tissues ◽  
Theoretic Concept ◽  
Tissue Size ◽  
Epithelial Sheets

Tracking of cells in live-imaging microscopy videos of epithelial sheets is a powerful tool for investigating fundamental processes in embryonic development. Characterizing cell growth, proliferation, intercalation and apoptosis in epithelia helps us to understand how morphogenetic processes such as tissue invagination and extension are locally regulated and controlled. Accurate cell tracking requires correctly resolving cells entering or leaving the field of view between frames, cell neighbour exchanges, cell removals and cell divisions. However, current tracking methods for epithelial sheets are not robust to large morphogenetic deformations and require significant manual interventions. Here, we present a novel algorithm for epithelial cell tracking, exploiting the graph-theoretic concept of a ‘maximum common subgraph’ to track cells between frames of a video. Our algorithm does not require the adjustment of tissue-specific parameters, and scales in sub-quadratic time with tissue size. It does not rely on precise positional information, permitting large cell movements between frames and enabling tracking in datasets acquired at low temporal resolution due to experimental constraints such as phototoxicity. To demonstrate the method, we perform tracking on the Drosophila embryonic epidermis and compare cell–cell rearrangements to previous studies in other tissues. Our implementation is open source and generally applicable to epithelial tissues.

scholarly journals Long-term in toto cell tracking using lightsheet microscopy of the zebrafish tailbud

2019 ◽  
Vol 3 ◽  
pp. 163
Author(s):  
Timothy Fulton ◽  
Martin O. Lenz ◽  
Leila Muresan ◽  
Toby Andrews ◽  
Courtney Lancaster ◽  
...  
Keyword(s):  
Temporal Resolution ◽  
Cell Tracking ◽  
Image Acquisition ◽  
Light Sheet ◽  
Field Of View ◽  
Image Capture ◽  
Acquisition Period ◽  
Global Movement ◽  
Microscope Stage

In toto light-sheet imaging allows the tracking of entire growing tissues with high spatial and temporal resolution for many hours. However, this technology requires a sample to be immobilised to ensure that the tissue of interest remains within the field of view throughout the image acquisition period. We have developed a method of mounting and image capture for long-term light-sheet imaging of a growing zebrafish tailbud from the 18 somite stage through to the end of somitogenesis. By tracking the global movement of the tailbud during image acquisition and feeding this back to the microscope stage, we are able to ensure that the growing tissue remains within the field of view throughout image acquisition. Here, we present three representative datasets of embryos in which all nuclei are labelled and tracked until the completion of somitogenesis.

scholarly journals Nakade — a graph theoretic concept in Go

2001 ◽  
Vol 235 (1-3) ◽  
pp. 385-397
Author(s):  
Tomoki Nakamigawa
Keyword(s):  
Graph Theoretic ◽  
Theoretic Concept

Robustness of Regular Caterpillars

2017 ◽  
Vol 28 (07) ◽  
pp. 835-841 ◽  
Author(s):  
Aysun Aytaç ◽  
Zeynep Nihan Odabaş Berberler
Keyword(s):  
Computer Networks ◽  
Network Topology ◽  
Network Robustness ◽  
Graph Theoretic ◽  
Theoretic Concept

Robustness of the network topology is a key aspect in the design of computer networks. Vertex residual closeness is a new graph-theoretic concept defined as a measure of network robustness. In this model, edges are perfectly reliable and the vertices fail independently of each other. In this paper, vertex residual closeness of paths and regular caterpillars are calculated by giving an insight of how to evaluate the vertex residual closeness of path-like graphs.

scholarly journals In Vivo Cell Tracking and Cleared Tissue Imaging with Extended Field of View Selective Plane Illumination Microscopy

2019 ◽  
Vol 116 (3) ◽  
pp. 566a
Author(s):  
Leonardo A. Saunders ◽  
Devin Pace ◽  
Arianna Gentile ◽  
Dominik Stich ◽  
Angeles B. Ribera ◽  
...  
Keyword(s):  
Cell Tracking ◽  
Field Of View ◽  
Tissue Imaging ◽  
Selective Plane Illumination Microscopy ◽  
Extended Field ◽  
Extended Field Of View

scholarly journals Untwisting the Caenorhabditis elegans embryo

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Ryan Patrick Christensen ◽  
Alexandra Bokinsky ◽  
Anthony Santella ◽  
Yicong Wu ◽  
Javier Marquina-Solis ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Cell Tracking ◽  
Positional Information ◽  
Supplementary File ◽  
Cell Nuclei ◽  
C Elegans ◽  
Seam Cell ◽  
Late Embryogenesis ◽  
Embryonic Nervous System ◽  
Supplementary Material

The nematode Caenorhabditis elegans possesses a simple embryonic nervous system with few enough neurons that the growth of each cell could be followed to provide a systems-level view of development. However, studies of single cell development have largely been conducted in fixed or pre-twitching live embryos, because of technical difficulties associated with embryo movement in late embryogenesis. We present open-source untwisting and annotation software (http://mipav.cit.nih.gov/plugin_jws/mipav_worm_plugin.php) that allows the investigation of neurodevelopmental events in late embryogenesis and apply it to track the 3D positions of seam cell nuclei, neurons, and neurites in multiple elongating embryos. We also provide a tutorial describing how to use the software (<xref ref-type="supplementary-material" rid="SD1-data">Supplementary file 1</xref>) and a detailed description of the untwisting algorithm (Appendix). The detailed positional information we obtained enabled us to develop a composite model showing movement of these cells and neurites in an 'average' worm embryo. The untwisting and cell tracking capabilities of our method provide a foundation on which to catalog C. elegans neurodevelopment, allowing interrogation of developmental events in previously inaccessible periods of embryogenesis.

scholarly journals Long-term in toto cell tracking using lightsheet microscopy of the zebrafish tailbud

2018 ◽  
Vol 3 ◽  
pp. 163
Author(s):  
Timothy Fulton ◽  
Martin O. Lenz ◽  
Leila Muresan ◽  
Courtney Lancaster ◽  
Elizabeth Horton ◽  
...  
Keyword(s):  
Temporal Resolution ◽  
Cell Tracking ◽  
Image Acquisition ◽  
Light Sheet ◽  
Field Of View ◽  
Image Capture ◽  
Acquisition Period ◽  
Global Movement ◽  
Microscope Stage

In toto light-sheet imaging allows the tracking of entire growing tissues with high spatial and temporal resolution for many hours. However, this technology requires a sample to be immobilised to ensure that the tissue of interest remains within the field of view throughout the image acquisition period. We have developed a method of mounting and image capture for long-term light-sheet imaging of a growing zebrafish tailbud from the 18 somite stage through to the end of somitogenesis. By tracking the global movement of the tailbud during image acquisition and feeding this back to the microscope stage, we are able to ensure that the growing tissue remains within the field of view throughout image acquisition. Here, we present three representative datasets of embryos in which all nuclei are labelled and tracked until the completion of somitogenesis.

Link-Centre and Indexes of a Kinematic Chain

1992 ◽  
Author(s):  
V. P. Agrawal ◽  
J. N. Yadav ◽  
C. R. Pratap
Keyword(s):  
Kinematic Chain ◽  
Degree Of Freedom ◽  
Input Output ◽  
Function Generator ◽  
Kinematic Chains ◽  
Graph Theoretic ◽  
Optimum Selection ◽  
Theoretic Concept ◽  
Selection Of

Abstract A new graph theoretic concept of link-centre of a kinematic chain is introduced. The link-centre of a kinematic chain is defined as a subset of set of links of the kinematic chain using a hierarchy of criteria based on distance concept. A number of structural invariants are defined for a kinematic chain which may be used for identification and classification of kinematic chains and mechanisms. An algorithm is developed on the basis of the concept of distance and the link-centre for optimum selection of input, output and fixed links in a multi-degree-of-freedom function generator.

scholarly journals On Buckling Morphogenesis

2016 ◽  
Vol 138 (2) ◽  
Author(s):  
Celeste M. Nelson
Keyword(s):  
Three Dimensional ◽  
Mechanical Forces ◽  
Two Dimensional ◽  
One Dimensional ◽  
Epithelial Tissues ◽  
Epithelial Sheets ◽  
The Brain ◽  
Epithelial Tubes

Cell-generated mechanical forces drive many of the tissue movements and rearrangements that are required to transform simple populations of cells into the complex three-dimensional geometries of mature organs. However, mechanical forces do not need to arise from active cellular movements. Recent studies have illuminated the roles of passive forces that result from mechanical instabilities between epithelial tissues and their surroundings. These mechanical instabilities cause essentially one-dimensional epithelial tubes and two-dimensional epithelial sheets to buckle or wrinkle into complex topologies containing loops, folds, and undulations in organs as diverse as the brain, the intestine, and the lung. Here, I highlight examples of buckling and wrinkling morphogenesis, and suggest that this morphogenetic mechanism may be broadly responsible for sculpting organ form.

scholarly journals Cache Transition Systems for Graph Parsing

2018 ◽  
Vol 44 (1) ◽  
pp. 85-118 ◽  
Author(s):  
Daniel Gildea ◽  
Giorgio Satta ◽  
Xiaochang Peng
Keyword(s):  
Transition System ◽  
Tree Decomposition ◽  
Dependency Parsing ◽  
Semantic Parsing ◽  
Fixed Size ◽  
Transition Systems ◽  
Graph Theoretic ◽  
Theoretic Concept ◽  
The Relationship

Motivated by the task of semantic parsing, we describe a transition system that generalizes standard transition-based dependency parsing techniques to generate a graph rather than a tree. Our system includes a cache with fixed size m, and we characterize the relationship between the parameter m and the class of graphs that can be produced through the graph-theoretic concept of tree decomposition. We find empirically that small cache sizes cover a high percentage of sentences in existing semantic corpora.

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