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 taxonomy
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...
Published in: | Journal of Phycology |
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Online Access: | https://epic.awi.de/id/eprint/48190/ https://epic.awi.de/id/eprint/48190/1/Beszteri_et_al-2018-Journal_of_Phycology.pdf https://hdl.handle.net/10013/epic.c82a098a-627e-4676-92bb-0b358a3a5aac |
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ftawi:oai:epic.awi.de:48190 2024-09-15T18:37:16+00:00 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 taxonomy Beszteri, Bank Allen, Claire Almandoz, Gastón O. Armand, L. Barcena, M. A. Cantzler, Hannelore Crosta, Xavier Esper, Oliver Jordan, R. W. Kauer, Gerhard Klaas, Christine Kloster, Michael Leventer, Amy Pike, J. Rigual Hernández, Andres S. 2018 application/pdf https://epic.awi.de/id/eprint/48190/ https://epic.awi.de/id/eprint/48190/1/Beszteri_et_al-2018-Journal_of_Phycology.pdf https://hdl.handle.net/10013/epic.c82a098a-627e-4676-92bb-0b358a3a5aac unknown Wiley https://epic.awi.de/id/eprint/48190/1/Beszteri_et_al-2018-Journal_of_Phycology.pdf Beszteri, B. orcid:0000-0002-6852-1588 , Allen, C. , Almandoz, G. O. , Armand, L. , Barcena, M. A. , Cantzler, H. , Crosta, X. , Esper, O. orcid:0000-0002-4342-3471 , Jordan, R. W. , Kauer, G. , Klaas, C. orcid:0000-0002-6679-8970 , Kloster, M. orcid:0000-0001-9244-4925 , Leventer, A. , Pike, J. and Rigual Hernández, A. S. (2018) 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 taxonomy , Journal of Phycology, 54 (5), pp. 703-719 . doi:10.1111/jpy.12767 <https://doi.org/10.1111/jpy.12767> , hdl:10013/epic.c82a098a-627e-4676-92bb-0b358a3a5aac EPIC3Journal of Phycology, Wiley, 54(5), pp. 703-719 Article isiRev 2018 ftawi https://doi.org/10.1111/jpy.12767 2024-06-24T04:21:00Z 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. Article in Journal/Newspaper Southern Ocean Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) Journal of Phycology 54 5 703 719 |
institution |
Open Polar |
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Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) |
op_collection_id |
ftawi |
language |
unknown |
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 |
Article in Journal/Newspaper |
author |
Beszteri, Bank Allen, Claire Almandoz, Gastón O. Armand, L. Barcena, M. A. Cantzler, Hannelore Crosta, Xavier Esper, Oliver Jordan, R. W. Kauer, Gerhard Klaas, Christine Kloster, Michael Leventer, Amy Pike, J. Rigual Hernández, Andres S. |
spellingShingle |
Beszteri, Bank Allen, Claire Almandoz, Gastón O. Armand, L. Barcena, M. A. Cantzler, Hannelore Crosta, Xavier Esper, Oliver Jordan, R. W. Kauer, Gerhard Klaas, Christine Kloster, Michael Leventer, Amy Pike, J. Rigual Hernández, Andres 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 taxonomy |
author_facet |
Beszteri, Bank Allen, Claire Almandoz, Gastón O. Armand, L. Barcena, M. A. Cantzler, Hannelore Crosta, Xavier Esper, Oliver Jordan, R. W. Kauer, Gerhard Klaas, Christine Kloster, Michael Leventer, Amy Pike, J. Rigual Hernández, Andres S. |
author_sort |
Beszteri, Bank |
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 taxonomy |
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 taxonomy |
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 taxonomy |
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 taxonomy |
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 taxonomy |
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 taxonomy |
publisher |
Wiley |
publishDate |
2018 |
url |
https://epic.awi.de/id/eprint/48190/ https://epic.awi.de/id/eprint/48190/1/Beszteri_et_al-2018-Journal_of_Phycology.pdf https://hdl.handle.net/10013/epic.c82a098a-627e-4676-92bb-0b358a3a5aac |
genre |
Southern Ocean |
genre_facet |
Southern Ocean |
op_source |
EPIC3Journal of Phycology, Wiley, 54(5), pp. 703-719 |
op_relation |
https://epic.awi.de/id/eprint/48190/1/Beszteri_et_al-2018-Journal_of_Phycology.pdf Beszteri, B. orcid:0000-0002-6852-1588 , Allen, C. , Almandoz, G. O. , Armand, L. , Barcena, M. A. , Cantzler, H. , Crosta, X. , Esper, O. orcid:0000-0002-4342-3471 , Jordan, R. W. , Kauer, G. , Klaas, C. orcid:0000-0002-6679-8970 , Kloster, M. orcid:0000-0001-9244-4925 , Leventer, A. , Pike, J. and Rigual Hernández, A. S. (2018) 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 taxonomy , Journal of Phycology, 54 (5), pp. 703-719 . doi:10.1111/jpy.12767 <https://doi.org/10.1111/jpy.12767> , hdl:10013/epic.c82a098a-627e-4676-92bb-0b358a3a5aac |
op_doi |
https://doi.org/10.1111/jpy.12767 |
container_title |
Journal of Phycology |
container_volume |
54 |
container_issue |
5 |
container_start_page |
703 |
op_container_end_page |
719 |
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1810481615783067648 |