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Robust cell tracking in epithelial tissues through identification of maximum common subgraphs
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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134023/ https://www.ncbi.nlm.nih.gov/pubmed/28334699 http://dx.doi.org/10.1098/rsif.2016.0725 |
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author | Kursawe, Jochen Bardenet, Rémi Zartman, Jeremiah J. Baker, Ruth E. Fletcher, Alexander G. |
author_facet | Kursawe, Jochen Bardenet, Rémi Zartman, Jeremiah J. Baker, Ruth E. Fletcher, Alexander G. |
author_sort | Kursawe, Jochen |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5134023 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | The Royal Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-51340232016-12-12 Robust cell tracking in epithelial tissues through identification of maximum common subgraphs Kursawe, Jochen Bardenet, Rémi Zartman, Jeremiah J. Baker, Ruth E. Fletcher, Alexander G. J R Soc Interface Life Sciences–Mathematics interface 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. The Royal Society 2016-11 /pmc/articles/PMC5134023/ /pubmed/28334699 http://dx.doi.org/10.1098/rsif.2016.0725 Text en © 2016 The Authors. http://creativecommons.org/licenses/by/4.0/ Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. |
spellingShingle | Life Sciences–Mathematics interface Kursawe, Jochen Bardenet, Rémi Zartman, Jeremiah J. Baker, Ruth E. Fletcher, Alexander G. Robust cell tracking in epithelial tissues through identification of maximum common subgraphs |
title | Robust cell tracking in epithelial tissues through identification of maximum common subgraphs |
title_full | Robust cell tracking in epithelial tissues through identification of maximum common subgraphs |
title_fullStr | Robust cell tracking in epithelial tissues through identification of maximum common subgraphs |
title_full_unstemmed | Robust cell tracking in epithelial tissues through identification of maximum common subgraphs |
title_short | Robust cell tracking in epithelial tissues through identification of maximum common subgraphs |
title_sort | robust cell tracking in epithelial tissues through identification of maximum common subgraphs |
topic | Life Sciences–Mathematics interface |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134023/ https://www.ncbi.nlm.nih.gov/pubmed/28334699 http://dx.doi.org/10.1098/rsif.2016.0725 |
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