On the 3D reconstruction of diatom frustules: a novel method, applications, and limitations

Abstract

Because of the importance of diatoms and the lack of information about their third dimension, a new method for the 3D reconstruction is explored, based on digital image correlation of several scanning electron microscope images. The accuracy of the method to reconstruct both centric and pennate (symmetrical and asymmetrical) diatoms was shown, independently of valve size and shape, and considering not only the general frustule morphology but also the intricate ornamentation. Several measurements were obtained, such as of the surface and projected areas and the valve volume. These results were validated by focused ion beam transverse cross section of one valve, and the quantitative results were compared with geometric models commonly applied. Furthermore, direct volume calculations based on 3D reconstructions have several advantages, such as it has higher taxonomic accuracy than the methods based on light microscopy; it solves the problems of the light halos; it allows the precise measurement of all linear dimensions, including the often neglected third dimension; natural samples can be measured directly; and it provides an exact estimate of cell volume, independently of its shape or alterations due to life cycle stage. This approach provides therefore a simple way to measure the morphological features of diatoms, even at a nanoscale, and can be applied to other microorganisms commonly illustrated by means of scanning electron microscopy.

Segmentation-free image processing and analysis of precipitate shapes in 2D and 3D

“…The inspiration to our current work was the success that shape analysis enjoyed with these segmentation-free feature descriptors. There are, however, reconstruction-based imaging techniques that can directly lead to easier to segment datasets [21,22] as compared to the simple micrographs used here.…”

Diatom and Diatomite: Different Focus on Natural Media to Material Science Path

“…Living diatoms is a major part of Earth's biomass and ecosystem since they consume from aqueous media more than 6.7 billion metric tons of silicon [1] and about 10 billion metric tons of CO 2 (equivalent to all of the world's rainforests activity) [2], per year respectively. Behaving like plants, diatoms produce chemical energy from light through photosynthesis and have specific anatomy since they are cells surrounded by a "glassy" porous wall [3] [4] [5]. This wall, called frustule, is made of amorphous silica in central or penal asbox nanostructured with porous pattern able to protect living cell from outside aggression and enabling, in the same time, nutriment sourcing [6] [7].…”