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...
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ftanucanberra:oai:openresearch-repository.anu.edu.au:1885/160388 2024-01-14T10:10:52+01:00 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 S. Almandoz, Gaston O Armand, Leanne Barcena, Maria Angeles Cantzler, Hannelore Crosta, Xavier Esper, O Jordan, Richard W Kauer, Gerhard Klaas, Christine application/pdf http://hdl.handle.net/1885/160388 https://doi.org/10.1111/jpy.12767 https://openresearch-repository.anu.edu.au/bitstream/1885/160388/5/01_Beszteri_Quantitative_comparison_of_2018.pdf.jpg en_AU eng Blackwell Publishing Ltd 0022-3646 http://hdl.handle.net/1885/160388 doi:10.1111/jpy.12767 https://openresearch-repository.anu.edu.au/bitstream/1885/160388/5/01_Beszteri_Quantitative_comparison_of_2018.pdf.jpg © 2018 The Authors Journal of Phycology published by Wiley Periodicals, Inc. on behalf of Phycological Society of America Journal of Phycology Journal article ftanucanberra https://doi.org/10.1111/jpy.12767 2023-12-15T09:36:03Z 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 Australian National University: ANU Digital Collections Southern Ocean Journal of Phycology 54 5 703 719 |
institution |
Open Polar |
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Australian National University: ANU Digital Collections |
op_collection_id |
ftanucanberra |
language |
English |
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 S. Almandoz, Gaston O Armand, Leanne Barcena, Maria Angeles Cantzler, Hannelore Crosta, Xavier Esper, O Jordan, Richard W Kauer, Gerhard Klaas, Christine |
spellingShingle |
Beszteri, Bank Allen, Claire S. Almandoz, Gaston O Armand, Leanne Barcena, Maria Angeles Cantzler, Hannelore Crosta, Xavier Esper, O Jordan, Richard W Kauer, Gerhard Klaas, Christine 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 S. Almandoz, Gaston O Armand, Leanne Barcena, Maria Angeles Cantzler, Hannelore Crosta, Xavier Esper, O Jordan, Richard W Kauer, Gerhard Klaas, Christine |
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 |
Blackwell Publishing Ltd |
url |
http://hdl.handle.net/1885/160388 https://doi.org/10.1111/jpy.12767 https://openresearch-repository.anu.edu.au/bitstream/1885/160388/5/01_Beszteri_Quantitative_comparison_of_2018.pdf.jpg |
geographic |
Southern Ocean |
geographic_facet |
Southern Ocean |
genre |
Southern Ocean |
genre_facet |
Southern Ocean |
op_source |
Journal of Phycology |
op_relation |
0022-3646 http://hdl.handle.net/1885/160388 doi:10.1111/jpy.12767 https://openresearch-repository.anu.edu.au/bitstream/1885/160388/5/01_Beszteri_Quantitative_comparison_of_2018.pdf.jpg |
op_rights |
© 2018 The Authors Journal of Phycology published by Wiley Periodicals, Inc. on behalf of Phycological Society of America |
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 |
_version_ |
1788065723656962048 |