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Cell-shape

MATLAB and Python source codes for calculating volume, surface area and other geometric characteristics of various geometric shapes. 

File "../data/CellSamples.xlsx" contains data samples with linear dimensions of plankton cells with different geometry. The Shape ID in this file correspond to the shape ID in the shape atlas http://phytobioimaging.unisalento.it/Products/AtlasOfShapes.aspx?ID_Tipo=0 and also in CalculationsOfCellVolume&Surface.pdf

To derive formulas for the surface area and volume we use a Maple script CellVolumeand Surface.mw.  This script was also saved as CalculationsOfCellVolume&Surface.pdf in case you do not have Maple. 

If you use this file please cite

Alexey Ryabov, Onur Kerimoglu, Elena Litchman, Irina Olenina, Leonilde Roselli, Alberto Basset, Elena Stanca, Bernd Blasius. "Shape matters: cell geometry determines phytoplankton diversity" bioRxiv 2020.02.06.937219; doi: https://doi.org/10.1101/2020.02.06.937219

Description

Main Scripts:

matlab/cellgeom.m

is a MATLAB script for calculating mean parameters. It takes data from "..\data\CellSamples.xlsx" and saves results into  "..\data\CellSamples_VA.xlsx". There is a flag, which allows to average linear dimensions for each species+location before calculating volume, area, etc. 

python/main.py & calc_cell_geom.py

are the equivalent Python (3.6) scripts, but they work at the moment for the datasets from Olenina et al., and not from Roselli et al.

Parameters calculated:

  • cell volume, V

  • cell surface area, A

  • equivalent radius of a sphere with the same volume,    

  • equivalent radius of a sphere with the same area

  • surface extension (inverse sphericity),

  • minimal, middle and maximal linear cell dimensions  (L_min, L_mid, L_max)

  • aspect ratio (r> for prolate cells and r<1 for oblate cells)

  • cell elongation class

    • prolate: r> 3/2, maximal cell dimensions exceeds the minimal dimension by more than 50%
    • compact: 2/3<r<3/2  (difference between linear dimensions is less than 50%)
    • oblate : r<2/3, maximal cell dimensions exceeds the minimal dimension by more than 50%