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KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs
Dynamic processes are ubiquitous and essential in living cells. To properly understand these processes, it is imperative to measure them in a time-dependent way and analyze the resulting data quantitatively, preferably with automated tools. Kymographs are single images that represent the motion of d...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The American Society for Cell Biology
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907728/ https://www.ncbi.nlm.nih.gov/pubmed/27099372 http://dx.doi.org/10.1091/mbc.E15-06-0404 |
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author | Mangeol, Pierre Prevo, Bram Peterman, Erwin J. G. |
author_facet | Mangeol, Pierre Prevo, Bram Peterman, Erwin J. G. |
author_sort | Mangeol, Pierre |
collection | PubMed |
description | Dynamic processes are ubiquitous and essential in living cells. To properly understand these processes, it is imperative to measure them in a time-dependent way and analyze the resulting data quantitatively, preferably with automated tools. Kymographs are single images that represent the motion of dynamic processes and are widely used in live-cell imaging. Although they contain the full range of dynamics, it is not straightforward to extract this quantitative information in a reliable way. Here we present two complementary, publicly available software tools, KymographClear and KymographDirect, that have the power to reveal detailed insight in dynamic processes. KymographClear is a macro toolset for ImageJ to generate kymographs that provides automatic color coding of the different directions of movement. KymographDirect is a stand-alone tool to extract quantitative information from kymographs obtained from a wide range of dynamic processes in an automated way, with high accuracy and reliability. We discuss the concepts behind these software tools, validate them using simulated data, and test them on experimental data. We show that these tools can be used to extract motility parameters from a diverse set of cell-biological experiments in an automated and user-friendly way. |
format | Online Article Text |
id | pubmed-4907728 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | The American Society for Cell Biology |
record_format | MEDLINE/PubMed |
spelling | pubmed-49077282016-08-30 KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs Mangeol, Pierre Prevo, Bram Peterman, Erwin J. G. Mol Biol Cell Articles Dynamic processes are ubiquitous and essential in living cells. To properly understand these processes, it is imperative to measure them in a time-dependent way and analyze the resulting data quantitatively, preferably with automated tools. Kymographs are single images that represent the motion of dynamic processes and are widely used in live-cell imaging. Although they contain the full range of dynamics, it is not straightforward to extract this quantitative information in a reliable way. Here we present two complementary, publicly available software tools, KymographClear and KymographDirect, that have the power to reveal detailed insight in dynamic processes. KymographClear is a macro toolset for ImageJ to generate kymographs that provides automatic color coding of the different directions of movement. KymographDirect is a stand-alone tool to extract quantitative information from kymographs obtained from a wide range of dynamic processes in an automated way, with high accuracy and reliability. We discuss the concepts behind these software tools, validate them using simulated data, and test them on experimental data. We show that these tools can be used to extract motility parameters from a diverse set of cell-biological experiments in an automated and user-friendly way. The American Society for Cell Biology 2016-06-15 /pmc/articles/PMC4907728/ /pubmed/27099372 http://dx.doi.org/10.1091/mbc.E15-06-0404 Text en © 2016 Mangeol et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0). “ASCB®,” “The American Society for Cell Biology®,” and “Molecular Biology of the Cell®” are registered trademarks of The American Society for Cell Biology. |
spellingShingle | Articles Mangeol, Pierre Prevo, Bram Peterman, Erwin J. G. KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs |
title | KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs |
title_full | KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs |
title_fullStr | KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs |
title_full_unstemmed | KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs |
title_short | KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs |
title_sort | kymographclear and kymographdirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907728/ https://www.ncbi.nlm.nih.gov/pubmed/27099372 http://dx.doi.org/10.1091/mbc.E15-06-0404 |
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