Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8
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| Format: | Dataset Open Access |
| Sprache: | en |
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2017
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| _version_ | 1867170997919023104 |
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| author | Kloster, Michael Esper, Oliver Kauer, Gerhard Beszteri, Bánk |
| author_facet | Kloster, Michael Esper, Oliver Kauer, Gerhard Beszteri, Bánk |
| collection | Datos científicos de ciencias marinas y ambientales |
| contents | 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 describe our workflow and give an overview of factors critical for success, ranging from preparation and mounting through slide scanning and autofocus finding to final morphometric data extraction. To demonstrate the usability of our methods we finally provide an example application by analysing Fragilariopsis kerguelensis valves originating from a sediment core, which substantially extends the size range reported in the literature. |
| format | Dataset Open Access |
| id | pangaea_https___doi_org_10_1594_PANGAEA_873993 |
| institution | PANGAEA |
| language | en |
| publishDate | 2017 |
| publisher | PANGAEA |
| record_format | pangaea |
| spellingShingle | Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8 Kloster, Michael Esper, Oliver Kauer, Gerhard Beszteri, Bánk ANT-VIII/3; Automated microscopy and image analysis workflow (Kloster et al. 2017); DEPTH, sediment/rock; File name; Fragilariopsis kerguelensis valve, height; Fragilariopsis kerguelensis valve, width; Gravity corer (Kiel type); Index; Marine isotopic stage; Method comment; Polarstern; Priority Programme 1158 Antarctic Research with Comparable Investigations in Arctic Sea Ice Areas; PS16; PS16/311; PS1768-8; Sample ID; Shona Ridge; SL; SPP1158 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 describe our workflow and give an overview of factors critical for success, ranging from preparation and mounting through slide scanning and autofocus finding to final morphometric data extraction. To demonstrate the usability of our methods we finally provide an example application by analysing Fragilariopsis kerguelensis valves originating from a sediment core, which substantially extends the size range reported in the literature. |
| title | Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8 |
| topic | ANT-VIII/3; Automated microscopy and image analysis workflow (Kloster et al. 2017); DEPTH, sediment/rock; File name; Fragilariopsis kerguelensis valve, height; Fragilariopsis kerguelensis valve, width; Gravity corer (Kiel type); Index; Marine isotopic stage; Method comment; Polarstern; Priority Programme 1158 Antarctic Research with Comparable Investigations in Arctic Sea Ice Areas; PS16; PS16/311; PS1768-8; Sample ID; Shona Ridge; SL; SPP1158 |
| url | https://doi.org/10.1594/PANGAEA.873993 |