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Appl. Sci. 2017, 7(4), 330;

Large-Scale Permanent Slide Imaging and Image Analysis for Diatom Morphometrics

Hustedt Diatom Study Centre, Section Polar Biological Oceanography, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
Hochschule Emden/Leer, Constantiaplatz 4, 26723 Emden, Germany
Author to whom correspondence should be addressed.
Academic Editors: Gabriel Cristobal, Saúl Blanco Lanza, Gloria Bueno and Jan Kybic
Received: 1 February 2017 / Revised: 16 March 2017 / Accepted: 23 March 2017 / Published: 28 March 2017
(This article belongs to the Special Issue Automated Analysis and Identification of Phytoplankton Images)
Full-Text   |   PDF [3490 KB, uploaded 29 March 2017]   |  


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. View Full-Text
Keywords: slide scanning; virtual slide; SHERPA; Fragilariopsis kerguelensis; microscopy; Metafer slide scanning; virtual slide; SHERPA; Fragilariopsis kerguelensis; microscopy; Metafer

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material

  • Externally hosted supplementary file 1
    Doi: (only for part of the supplementary material))
    Description: Settings for Metafer4 software, SHERPA settings und shape templates, R functions for reading SHERPA output and removing duplicates from each dataset, morphometric data from PS1768-8. The SHERPA software is available for download at

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Kloster, M.; Esper, O.; Kauer, G.; Beszteri, B. Large-Scale Permanent Slide Imaging and Image Analysis for Diatom Morphometrics. Appl. Sci. 2017, 7, 330.

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