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WormSizer: High-throughput Analysis of Nematode Size and Shape
The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3579787/ https://www.ncbi.nlm.nih.gov/pubmed/23451165 http://dx.doi.org/10.1371/journal.pone.0057142 |
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author | Moore, Brad T. Jordan, James M. Baugh, L. Ryan |
author_facet | Moore, Brad T. Jordan, James M. Baugh, L. Ryan |
author_sort | Moore, Brad T. |
collection | PubMed |
description | The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating volume either coarsely model the nematode as a cylinder or assume the worm shape or opacity is invariant. Our estimate is more robust to changes in morphology or optical density as it only assumes radial symmetry. This open source software is written as a plugin for the well-known image-processing framework Fiji/ImageJ. It may therefore be extended easily. We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series. We confirm quantitatively that a Dumpy (Dpy) mutant is short and fat and that a Long (Lon) mutant is long and thin. We show that daf-2 insulin-like receptor mutants are larger than wild-type upon hatching but grow slow, and WormSizer can distinguish dauer larvae from normal larvae. We also show that a Small (Sma) mutant is actually smaller than wild-type at all stages of larval development. WormSizer works with Uncoordinated (Unc) and Roller (Rol) mutants as well, indicating that it can be used with mutants despite behavioral phenotypes. We used our complete data set to perform a power analysis, giving users a sense of how many images are needed to detect different effect sizes. Our analysis confirms and extends on existing phenotypic characterization of well-characterized mutants, demonstrating the utility and robustness of WormSizer. |
format | Online Article Text |
id | pubmed-3579787 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-35797872013-02-28 WormSizer: High-throughput Analysis of Nematode Size and Shape Moore, Brad T. Jordan, James M. Baugh, L. Ryan PLoS One Research Article The fundamental phenotypes of growth rate, size and morphology are the result of complex interactions between genotype and environment. We developed a high-throughput software application, WormSizer, which computes size and shape of nematodes from brightfield images. Existing methods for estimating volume either coarsely model the nematode as a cylinder or assume the worm shape or opacity is invariant. Our estimate is more robust to changes in morphology or optical density as it only assumes radial symmetry. This open source software is written as a plugin for the well-known image-processing framework Fiji/ImageJ. It may therefore be extended easily. We evaluated the technical performance of this framework, and we used it to analyze growth and shape of several canonical Caenorhabditis elegans mutants in a developmental time series. We confirm quantitatively that a Dumpy (Dpy) mutant is short and fat and that a Long (Lon) mutant is long and thin. We show that daf-2 insulin-like receptor mutants are larger than wild-type upon hatching but grow slow, and WormSizer can distinguish dauer larvae from normal larvae. We also show that a Small (Sma) mutant is actually smaller than wild-type at all stages of larval development. WormSizer works with Uncoordinated (Unc) and Roller (Rol) mutants as well, indicating that it can be used with mutants despite behavioral phenotypes. We used our complete data set to perform a power analysis, giving users a sense of how many images are needed to detect different effect sizes. Our analysis confirms and extends on existing phenotypic characterization of well-characterized mutants, demonstrating the utility and robustness of WormSizer. Public Library of Science 2013-02-22 /pmc/articles/PMC3579787/ /pubmed/23451165 http://dx.doi.org/10.1371/journal.pone.0057142 Text en © 2013 Moore et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Moore, Brad T. Jordan, James M. Baugh, L. Ryan WormSizer: High-throughput Analysis of Nematode Size and Shape |
title | WormSizer: High-throughput Analysis of Nematode Size and Shape |
title_full | WormSizer: High-throughput Analysis of Nematode Size and Shape |
title_fullStr | WormSizer: High-throughput Analysis of Nematode Size and Shape |
title_full_unstemmed | WormSizer: High-throughput Analysis of Nematode Size and Shape |
title_short | WormSizer: High-throughput Analysis of Nematode Size and Shape |
title_sort | wormsizer: high-throughput analysis of nematode size and shape |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3579787/ https://www.ncbi.nlm.nih.gov/pubmed/23451165 http://dx.doi.org/10.1371/journal.pone.0057142 |
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