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Generalized box-plot for root growth ensembles
BACKGROUND: In the field of root biology there has been a remarkable progress in root phenotyping, which is the efficient acquisition and quantitative description of root morphology. What is currently missing are means to efficiently explore, exchange and present the massive amount of acquired, and...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333180/ https://www.ncbi.nlm.nih.gov/pubmed/28251866 http://dx.doi.org/10.1186/s12859-016-1445-3 |
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author | Vad, Viktor Cedrim, Douglas Busch, Wolfgang Filzmoser, Peter Viola, Ivan |
author_facet | Vad, Viktor Cedrim, Douglas Busch, Wolfgang Filzmoser, Peter Viola, Ivan |
author_sort | Vad, Viktor |
collection | PubMed |
description | BACKGROUND: In the field of root biology there has been a remarkable progress in root phenotyping, which is the efficient acquisition and quantitative description of root morphology. What is currently missing are means to efficiently explore, exchange and present the massive amount of acquired, and often time dependent root phenotypes. RESULTS: In this work, we present visual summaries of root ensembles by aggregating root images with identical genetic characteristics. We use the generalized box plot concept with a new formulation of data depth. In addition to spatial distributions, we created a visual representation to encode temporal distributions associated with the development of root individuals. CONCLUSIONS: The new formulation of data depth allows for much faster implementation close to interactive frame rates. This allows us to present the statistics from bootstrapping that characterize the root sample set quality. As a positive side effect of the new data-depth formulation we are able to define the geometric median for the curve ensemble, which was well received by the domain experts. |
format | Online Article Text |
id | pubmed-5333180 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-53331802017-03-06 Generalized box-plot for root growth ensembles Vad, Viktor Cedrim, Douglas Busch, Wolfgang Filzmoser, Peter Viola, Ivan BMC Bioinformatics Research BACKGROUND: In the field of root biology there has been a remarkable progress in root phenotyping, which is the efficient acquisition and quantitative description of root morphology. What is currently missing are means to efficiently explore, exchange and present the massive amount of acquired, and often time dependent root phenotypes. RESULTS: In this work, we present visual summaries of root ensembles by aggregating root images with identical genetic characteristics. We use the generalized box plot concept with a new formulation of data depth. In addition to spatial distributions, we created a visual representation to encode temporal distributions associated with the development of root individuals. CONCLUSIONS: The new formulation of data depth allows for much faster implementation close to interactive frame rates. This allows us to present the statistics from bootstrapping that characterize the root sample set quality. As a positive side effect of the new data-depth formulation we are able to define the geometric median for the curve ensemble, which was well received by the domain experts. BioMed Central 2017-02-15 /pmc/articles/PMC5333180/ /pubmed/28251866 http://dx.doi.org/10.1186/s12859-016-1445-3 Text en © The Author(s) 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Vad, Viktor Cedrim, Douglas Busch, Wolfgang Filzmoser, Peter Viola, Ivan Generalized box-plot for root growth ensembles |
title | Generalized box-plot for root growth ensembles |
title_full | Generalized box-plot for root growth ensembles |
title_fullStr | Generalized box-plot for root growth ensembles |
title_full_unstemmed | Generalized box-plot for root growth ensembles |
title_short | Generalized box-plot for root growth ensembles |
title_sort | generalized box-plot for root growth ensembles |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333180/ https://www.ncbi.nlm.nih.gov/pubmed/28251866 http://dx.doi.org/10.1186/s12859-016-1445-3 |
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