Citation:

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

Project(s):

Priority Programme 1158 Antarctic Research with Comparable Investigations in Arctic Sea Ice Areas (SPP1158)

Funding:

German Research Foundation (DFG), grant/award no. 5472008 : Priority Programme 1158 Antarctic Research with Comparable Investigations in Arctic Sea Ice Areas

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: (PS16) * Basis: * Method/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):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	DEPTH, sediment/rock	Depth sed	m	Beszteri, Bánk		Geocode
2	Sample ID	Sample ID		Beszteri, Bánk
3	File name	File name		Beszteri, Bánk	Automated microscopy and image analysis workflow (Kloster et al. 2017)	of raw data file
4	Fragilariopsis kerguelensis valve, width	F. kerguelensis w	µm	Beszteri, Bánk	Automated microscopy and image analysis workflow (Kloster et al. 2017)
5	Fragilariopsis kerguelensis valve, height	F. kerguelensis h	µm	Beszteri, Bánk	Automated microscopy and image analysis workflow (Kloster et al. 2017)
6	Method comment	Method comm		Beszteri, Bánk	Automated microscopy and image analysis workflow (Kloster et al. 2017)	Segmentation m
7	Index	Index		Beszteri, Bánk		Ranking Index indicates confidence in the segmentation results for the object measured; for more details, see doi:10.1186/1471-2105-15-218
8	Marine isotopic stage	MIS		Beszteri, Bánk

License:

Creative Commons Attribution 3.0 Unported (CC-BY-3.0)

Size:

83013 data points

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