The database of the diatom valve outlines

by

A.M. Lyakh1, S.G. Lelekov2

1A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, RF, Sevastopol, Nakhimov Av., 2

E–mail: me@antonlyakh.ru

2Sevastopol State University, RF, Sevastopol, Universitetskaya St., 33

E–mail: p1859@yandex.ru

DOI: 10.33075/2220-5861-2022-3-97-105

UDC 574.5+561.26:477.75(556.5)+004.65                                                   

Abstract:

   Diatoms are widespread microscopic aquatic autotrophs covered by a siliceous frustule. Diatom valves are large, clearly visible elements of the frustule. The outlines of the valves are used in many tasks: species identification, construction of geometric models of diatom frustules, assessment of the condition of water bodies, and as templates for systematization of microalgae images. To solve these tasks the samples of characteristic shapes of valves are needed. The paper presents the structure of a database for storing the outlines of diatom valves, considers ways of mathematical description of valve outlines and provides scenarios for interaction with the database.

   To mathematically describe the outline of the valves, we use cubic Bezier curves, smoothly fit together. We construct the outline from the photographs of diatom valves. We do not take into account pseudosymmetric deviations and construct perfect symmetric contours. We also calculate numerical shape descriptors, namely coefficients of elliptic Fourier transform, that are invariant to the size, position, and rotation of the original contour. The results are saved in the database.

   The database consists of tables for contours, contour names, contour descriptors, and notes about descriptors. The database interacts with external database of Arxip – the library of published microalgae images (3d-microalgae.org/arxip).

   The database access interface allows retrieving information on the shape by its unique identifier or name if the shape has a name. The information includes the descriptions of the curve bounding the valve and additional data.

   The database is available at 3d-microalgae.org/diatoms/valve-shapes

Keywords: shape analysis, morphological variability, teratological shapes, silhouettes database, classification, visual index, diatoms.

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