Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy1
Semiautomated methods for microscopic image acquisition, image analysis, and taxonomic identification have repeatedly received attention in diatom analysis. Less well studied is the question whether and how such methods might prove useful for clarifying the delimitation of species that are difficult...
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ftpubmed:oai:pubmedcentral.nih.gov:6220827 2023-05-15T18:25:32+02:00 Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy1 Beszteri, Bánk Allen, Claire Almandoz, Gastón O. Armand, Leanne Barcena, María Ángeles Cantzler, Hannelore Crosta, Xavier Esper, Oliver Jordan, Richard W. Kauer, Gerhard Klaas, Christine Kloster, Michael Leventer, Amy Pike, Jennifer Rigual Hernández, Andrés S. 2018-08-28 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6220827/ http://www.ncbi.nlm.nih.gov/pubmed/30014469 https://doi.org/10.1111/jpy.12767 en eng John Wiley and Sons Inc. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6220827/ http://www.ncbi.nlm.nih.gov/pubmed/30014469 http://dx.doi.org/10.1111/jpy.12767 © 2018 The Authors Journal of Phycology published by Wiley Periodicals, Inc. on behalf of Phycological Society of America This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. CC-BY Regular Articles Text 2018 ftpubmed https://doi.org/10.1111/jpy.12767 2018-11-18T02:09:29Z Semiautomated methods for microscopic image acquisition, image analysis, and taxonomic identification have repeatedly received attention in diatom analysis. Less well studied is the question whether and how such methods might prove useful for clarifying the delimitation of species that are difficult to separate for human taxonomists. To try to answer this question, three very similar Fragilariopsis species endemic to the Southern Ocean were targeted in this study: F. obliquecostata, F. ritscheri, and F. sublinearis. A set of 501 extended focus depth specimen images were obtained using a standardized, semiautomated microscopic procedure. Twelve diatomists independently identified these specimen images in order to reconcile taxonomic opinions and agree upon a taxonomic gold standard. Using image analyses, we then extracted morphometric features representing taxonomic characters of the target taxa. The discriminating ability of individual morphometric features was tested visually and statistically, and multivariate classification experiments were performed to test the agreement of the quantitatively defined taxa assignments with expert consensus opinion. Beyond an updated differential diagnosis of the studied taxa, our study also shows that automated imaging and image analysis procedures for diatoms are coming close to reaching a broad applicability for routine use. Text Southern Ocean PubMed Central (PMC) Southern Ocean Journal of Phycology 54 5 703 719 |
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Regular Articles Beszteri, Bánk Allen, Claire Almandoz, Gastón O. Armand, Leanne Barcena, María Ángeles Cantzler, Hannelore Crosta, Xavier Esper, Oliver Jordan, Richard W. Kauer, Gerhard Klaas, Christine Kloster, Michael Leventer, Amy Pike, Jennifer Rigual Hernández, Andrés S. Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy1 |
topic_facet |
Regular Articles |
description |
Semiautomated methods for microscopic image acquisition, image analysis, and taxonomic identification have repeatedly received attention in diatom analysis. Less well studied is the question whether and how such methods might prove useful for clarifying the delimitation of species that are difficult to separate for human taxonomists. To try to answer this question, three very similar Fragilariopsis species endemic to the Southern Ocean were targeted in this study: F. obliquecostata, F. ritscheri, and F. sublinearis. A set of 501 extended focus depth specimen images were obtained using a standardized, semiautomated microscopic procedure. Twelve diatomists independently identified these specimen images in order to reconcile taxonomic opinions and agree upon a taxonomic gold standard. Using image analyses, we then extracted morphometric features representing taxonomic characters of the target taxa. The discriminating ability of individual morphometric features was tested visually and statistically, and multivariate classification experiments were performed to test the agreement of the quantitatively defined taxa assignments with expert consensus opinion. Beyond an updated differential diagnosis of the studied taxa, our study also shows that automated imaging and image analysis procedures for diatoms are coming close to reaching a broad applicability for routine use. |
format |
Text |
author |
Beszteri, Bánk Allen, Claire Almandoz, Gastón O. Armand, Leanne Barcena, María Ángeles Cantzler, Hannelore Crosta, Xavier Esper, Oliver Jordan, Richard W. Kauer, Gerhard Klaas, Christine Kloster, Michael Leventer, Amy Pike, Jennifer Rigual Hernández, Andrés S. |
author_facet |
Beszteri, Bánk Allen, Claire Almandoz, Gastón O. Armand, Leanne Barcena, María Ángeles Cantzler, Hannelore Crosta, Xavier Esper, Oliver Jordan, Richard W. Kauer, Gerhard Klaas, Christine Kloster, Michael Leventer, Amy Pike, Jennifer Rigual Hernández, Andrés S. |
author_sort |
Beszteri, Bánk |
title |
Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy1 |
title_short |
Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy1 |
title_full |
Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy1 |
title_fullStr |
Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy1 |
title_full_unstemmed |
Quantitative comparison of taxa and taxon concepts in the diatom genus Fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy1 |
title_sort |
quantitative comparison of taxa and taxon concepts in the diatom genus fragilariopsis: a case study on using slide scanning, multiexpert image annotation, and image analysis in taxonomy1 |
publisher |
John Wiley and Sons Inc. |
publishDate |
2018 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6220827/ http://www.ncbi.nlm.nih.gov/pubmed/30014469 https://doi.org/10.1111/jpy.12767 |
geographic |
Southern Ocean |
geographic_facet |
Southern Ocean |
genre |
Southern Ocean |
genre_facet |
Southern Ocean |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6220827/ http://www.ncbi.nlm.nih.gov/pubmed/30014469 http://dx.doi.org/10.1111/jpy.12767 |
op_rights |
© 2018 The Authors Journal of Phycology published by Wiley Periodicals, Inc. on behalf of Phycological Society of America This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1111/jpy.12767 |
container_title |
Journal of Phycology |
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54 |
container_issue |
5 |
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703 |
op_container_end_page |
719 |
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1766207053459619840 |