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Kloster, Michael; Esper, Oliver; Kauer, Gerhard; Beszteri, Bánk (2017): Length and width measurements of Fragilariopsis kerguelensis valves from sediment core PS1768-8. PANGAEA, https://doi.org/10.1594/PANGAEA.873993, Supplement to: Kloster, M et al. (2017): Large scale permanent slide imaging and image analysis for diatom morphometrics. Applied Sciences, 7(4), 330, https://doi.org/10.3390/app7040330

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Abstract:
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.
Related to:
Kloster, Michael; Kauer, Gerhard; Beszteri, Bánk (2014): Fragilariopsis kerguelensis images from sediment core PS1768-8. Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, PANGAEA, https://doi.org/10.1594/PANGAEA.833665
Coverage:
Latitude: -52.593000 * Longitude: 4.476000
Date/Time Start: 1989-11-11T21:40:00 * Date/Time End: 1989-11-11T21:40:00
Minimum DEPTH, sediment/rock: 0.6 m * Maximum DEPTH, sediment/rock: 8.7 m
Event(s):
PS1768-8 (PS16/311) * Latitude: -52.593000 * Longitude: 4.476000 * Date/Time: 1989-11-11T21:40:00 * Elevation: -3299.0 m * Recovery: 8.96 m * Location: Shona Ridge * Campaign: ANT-VIII/3 (PS16) * Basis: Polarstern * Device: Gravity corer (Kiel type) (SL) * Comment: 10 core sections: 0-0.44, 0.44-1.06, 1.06-2.06, 2.06-3.06, 3.06-4.06, 4.06-5.04, 5.04-6.04, 6.04-7.04, 7.04-8.04, 8.04-8.96 m
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethodComment
1DEPTH, sediment/rockDepthmBeszteri, BánkGeocode
2Sample IDSample IDBeszteri, Bánk
3File nameFile nameBeszteri, BánkAutomated microscopy and image analysis workflow (Kloster et al. 2017)of raw data file
4Fragilariopsis kerguelensis valve, widthF. kerguelensis wµmBeszteri, BánkAutomated microscopy and image analysis workflow (Kloster et al. 2017)
5Fragilariopsis kerguelensis valve, heightF. kerguelensis hµmBeszteri, BánkAutomated microscopy and image analysis workflow (Kloster et al. 2017)
6Method commentMethod commBeszteri, BánkAutomated microscopy and image analysis workflow (Kloster et al. 2017)Segmentation m
7IndexIndexBeszteri, BánkRanking Index indicates confidence in the segmentation results for the object measured; for more details, see doi:10.1186/1471-2105-15-218
8Marine isotopic stageMISBeszteri, Bánk
Size:
83013 data points

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