Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8 ...
Light microscopy analysis of diatom frustules is widely used in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. Although there is a need for automation in these applications, various developments in image processing and analysis...
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ftdatacite:10.1594/pangaea.873993 2023-10-01T03:51:10+02:00 Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8 ... Kloster, Michael Esper, Oliver Kauer, Gerhard Beszteri, Bánk 2017 text/tab-separated-values https://dx.doi.org/10.1594/pangaea.873993 https://doi.pangaea.de/10.1594/PANGAEA.873993 en eng PANGAEA https://dx.doi.org/10.3390/app7040330 https://dx.doi.org/10.1594/pangaea.833665 Creative Commons Attribution 3.0 Unported https://creativecommons.org/licenses/by/3.0/legalcode cc-by-3.0 DEPTH, sediment/rock Sample ID File name Fragilariopsis kerguelensis valve, width Fragilariopsis kerguelensis valve, height Method comment Index Marine isotopic stage Gravity corer Kiel type Automated microscopy and image analysis workflow Kloster et al. 2017 ANT-VIII/3 Polarstern Priority Programme 1158 Antarctic Research with Comparable Investigations in Arctic Sea Ice Areas SPP1158 Dataset Supplementary Dataset dataset 2017 ftdatacite https://doi.org/10.1594/pangaea.87399310.3390/app704033010.1594/pangaea.833665 2023-09-04T14:52:34Z Light microscopy analysis of diatom frustules is widely used in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. Although there is a need for automation in these applications, various developments in image processing and analysis methodology supporting these tasks have not become widespread in diatom-based analyses. We have addressed this issue by combining our automated diatom image analysis software SHERPA with a commercial slide-scanning microscope. The resulting workflow enables mass-analyses of a broad range of morphometric features from individual frustules mounted on permanent slides. Extensive automation and internal quality control of the results helps to minimize user intervention, but care was taken to allow the user to stay in control of the most critical steps (exact segmentation of valve outlines and selection of objects of interest) using interactive functions for reviewing and revising results. In this contribution, we ... : Supplement to: Kloster, Michael; Esper, Oliver; Kauer, Gerhard; Beszteri, Bánk (2017): Large scale permanent slide imaging and image analysis for diatom morphometrics. Applied Sciences, 7(4), 330 ... Dataset Antarc* Antarctic Arctic Sea ice DataCite Metadata Store (German National Library of Science and Technology) Arctic Antarctic |
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Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
DEPTH, sediment/rock Sample ID File name Fragilariopsis kerguelensis valve, width Fragilariopsis kerguelensis valve, height Method comment Index Marine isotopic stage Gravity corer Kiel type Automated microscopy and image analysis workflow Kloster et al. 2017 ANT-VIII/3 Polarstern Priority Programme 1158 Antarctic Research with Comparable Investigations in Arctic Sea Ice Areas SPP1158 |
spellingShingle |
DEPTH, sediment/rock Sample ID File name Fragilariopsis kerguelensis valve, width Fragilariopsis kerguelensis valve, height Method comment Index Marine isotopic stage Gravity corer Kiel type Automated microscopy and image analysis workflow Kloster et al. 2017 ANT-VIII/3 Polarstern Priority Programme 1158 Antarctic Research with Comparable Investigations in Arctic Sea Ice Areas SPP1158 Kloster, Michael Esper, Oliver Kauer, Gerhard Beszteri, Bánk Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8 ... |
topic_facet |
DEPTH, sediment/rock Sample ID File name Fragilariopsis kerguelensis valve, width Fragilariopsis kerguelensis valve, height Method comment Index Marine isotopic stage Gravity corer Kiel type Automated microscopy and image analysis workflow Kloster et al. 2017 ANT-VIII/3 Polarstern Priority Programme 1158 Antarctic Research with Comparable Investigations in Arctic Sea Ice Areas SPP1158 |
description |
Light microscopy analysis of diatom frustules is widely used in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. Although there is a need for automation in these applications, various developments in image processing and analysis methodology supporting these tasks have not become widespread in diatom-based analyses. We have addressed this issue by combining our automated diatom image analysis software SHERPA with a commercial slide-scanning microscope. The resulting workflow enables mass-analyses of a broad range of morphometric features from individual frustules mounted on permanent slides. Extensive automation and internal quality control of the results helps to minimize user intervention, but care was taken to allow the user to stay in control of the most critical steps (exact segmentation of valve outlines and selection of objects of interest) using interactive functions for reviewing and revising results. In this contribution, we ... : Supplement to: Kloster, Michael; Esper, Oliver; Kauer, Gerhard; Beszteri, Bánk (2017): Large scale permanent slide imaging and image analysis for diatom morphometrics. Applied Sciences, 7(4), 330 ... |
format |
Dataset |
author |
Kloster, Michael Esper, Oliver Kauer, Gerhard Beszteri, Bánk |
author_facet |
Kloster, Michael Esper, Oliver Kauer, Gerhard Beszteri, Bánk |
author_sort |
Kloster, Michael |
title |
Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8 ... |
title_short |
Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8 ... |
title_full |
Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8 ... |
title_fullStr |
Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8 ... |
title_full_unstemmed |
Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8 ... |
title_sort |
length and width measurements of fragilariopsis kerguelensis valves from sediment core ps1768-8 ... |
publisher |
PANGAEA |
publishDate |
2017 |
url |
https://dx.doi.org/10.1594/pangaea.873993 https://doi.pangaea.de/10.1594/PANGAEA.873993 |
geographic |
Arctic Antarctic |
geographic_facet |
Arctic Antarctic |
genre |
Antarc* Antarctic Arctic Sea ice |
genre_facet |
Antarc* Antarctic Arctic Sea ice |
op_relation |
https://dx.doi.org/10.3390/app7040330 https://dx.doi.org/10.1594/pangaea.833665 |
op_rights |
Creative Commons Attribution 3.0 Unported https://creativecommons.org/licenses/by/3.0/legalcode cc-by-3.0 |
op_doi |
https://doi.org/10.1594/pangaea.87399310.3390/app704033010.1594/pangaea.833665 |
_version_ |
1778532512315736064 |