Next Article in Journal
Simulation of Permanent Deformation in High-Modulus Asphalt Pavement with Sloped and Horizontally Curved Alignment
Next Article in Special Issue
Automated Diatom Classification (Part B): A Deep Learning Approach
Previous Article in Journal
Collision Avoidance for Cooperative UAVs with Rolling Optimization Algorithm Based on Predictive State Space
Open AccessArticle

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

1
Hustedt Diatom Study Centre, Section Polar Biological Oceanography, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
2
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
Appl. Sci. 2017, 7(4), 330; https://doi.org/10.3390/app7040330
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)
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
Show Figures

Figure 1

MDPI and ACS Style

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

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map

1
  • Externally hosted supplementary file 1
    Doi: https://doi.org/10.1594/PANGAEA.873993 (only for part of the supplementary material))
    Link: http://awi.de/sherpa
    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 http://awi.de/sherpa
Back to TopTop