New data‐driven method from 3D confocal microscopy for calculating phytoplankton cell biovolume

Abstract

Confocal laser scanner microscopy coupled with an image analysis system was used to directly determine the shape and calculate the biovolume of phytoplankton organisms by constructing 3D models of cells. The study was performed on Biceratium furca (Ehrenberg) Vanhoeffen, which is one of the most complex-shaped phytoplankton. Traditionally, biovolume is obtained from a standardized set of geometric models based on linear dimensions measured by light microscopy. However, especially in the case of complex-shaped cells, biovolume is affected by very large errors associated with the numerous manual measurements that this entails. We evaluate the accuracy of these traditional methods by comparing the results obtained using geometric models with direct biovolume measurement by image analysis. Our results show cell biovolume measurement based on decomposition into simple geometrical shapes can be highly inaccurate. Although we assume that the most accurate cell shape is obtained by 3D direct biovolume measurement, which is based on voxel counting, the intrinsic uncertainty of this method is explored and assessed. Finally, we implement a data-driven formula-based approach to the calculation of biovolume of this complex-shaped organism. On one hand, the model is obtained from 3D direct calculation. On the other hand, it is based on just two linear dimensions which can easily be measured by hand. This approach has already been used for investigating the complexities of morphology and for determining the 3D structure of cells. It could also represent a novel way to generalize scaling laws for biovolume calculation.

Generating open-source 3D phytoplankton models by integrating photogrammetry with scanning electron microscopy

“…Cell morphology, typically characterized by surface area and biovolume, plays an important role in how efficiently cells can absorb nutrients and light. Numerous methodologies have been employed to calculate surface area and biovolume for phytoplankton, ranging from simplistic geometric models to 2D imaging and realistic 3D models (Hillebrand et al, 1999 ; Sun and Liu, 2003 ; Moberg and Sosik, 2012 ; Roselli et al, 2015 ; Borics et al, 2021 ; Mohan et al, 2021 ).…”

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

“…This result is explained by the larger level of detail obtained with our method. Also Roselli et al (2013Roselli et al ( , 2015 observed that direct volume estimation based on confocal microscopy coupled with an image analysis system seems to be more accurate than geometric models based on linear dimensions measured by light microscopy, since these are subject to substantial systematic errors. The differences between the values obtained by both methods can be also caused by the difficulties in selecting the most appropriate geometric shape, as pointed out also by Roselli et al (2013).…”

Multidirectional Image Sensing for Microscopy Based on a Rotatable Robot

“…To extend the FOV of the microscope and to get more image information, some novel microscopes have recently been developed, including the confocal microscope, dual-beam electron microscope (EM), cryo-electron microscope and so on. For instance, confocal microscopy is able to scan half-transparent objects layer-by-layer and then construct a 3D image [ 8 , 9 ]; the dual-beam EM can provide 3D image information by an etching-scanning process [ 10 , 11 ]; the cryo-EM allows one to construct the 3D structures of protein at atom scale [ 12 , 13 ]. Although these techniques have been successfully used in some specific fields, when it comes to multidirectional image sensing, these methods either destroy the samples permanently or have special sample preprocessing requirements.…”