DOI: 10.5061/dryad.wdbrv15vf
title: Micro-CT data and associated MATLAB scripts from the skeleton of the sea urchin Cidaris rugosa at four different resolutions

description: The sponge-like biomineralised calcite materials found in echinoderm
 skeletons are of interest in terms of both structure formation
 and biological function. Despite their crystalline atomic
 structure, they exhibit curved interfaces that have been related
 to known triply-periodic minimal surfaces. Here, we investigate
 the endoskeleton of the sea urchin Cidaris rugosa that has
 long been known to form a microstructure related to the Primitive
 surface. Using X-ray tomography, we find that the endoskeleton is
 organised as a composite material consisting of domains of
 bicontinuous microstructures with different structural
 properties. We describe, for the first time, the co-occurrence
 of ordered Primitive and Diamond structures and of a disordered
 structure within a single skeletal plate. We show that these
 structures can be distinguished by structural properties
 including solid volume fraction, trabeculae width, and to a
 lesser extent, interface area and mean curvature. In doing so, we
 present a robust method that extracts interface areas and
 curvature integrals from voxelized datasets using the Steiner
 polynomial for parallel body volumes. We discuss these very large
 scale bicontinuous structures in the context of their function,
 formation, and evolution.
description: Urchin samples were scanned with a Versa 520 XRM (Zeiss,
 Pleasanton, CA, USA) running Scout and Scan software (v15.0.17350.39816)
 at the Centre for Microscopy, Characterisation, and Analysis at the
 University of Western Australia. The whole urchin was scanned with a
 voltage of 65 kV at a magnification of 0.4X using the LE3 source filter
 delivering an isotropic voxel size of 22.8 μm. The sectioned
 interambulacral plate was scanned with a voltage of 80 kV at a
 magnification of 4X using the LE2 source filter delivering an isotropic
 voxel size of 3.72 μm. Two higher magnification scans were also conducted
 on an inner section of the interambulacral plate using a voltage of 80 kV,
 a magnfication of 4X, and the LE2 filter, delivering isotropic voxel sizes
 of 1.69 μm and 732 nm. Raw projection data were reconstructed using XRM
 Reconstructor software (v15.0.17350.39816) following a standard centre
 shift and beam hardening correction.
description: # Micro-CT data and MATLAB scripts for analysis of the skeleton of the sea
 urchin Cidaris rugosa at four different resolutions
 ## Description of the data
 and file structure This is tomography data from a Cidaris rugosa specimen.
 There are four datasets of different resolutions that have been uploaded
 in 3D tif format: whole urchin (voxel size = 22.8 um), interambulacral
 plate (voxel size = 3.72 um), inner interambulacral plate 1 (voxel size =
 1.69 um), and inner interambulacral plate 2 (voxel size = 732 nm). ##
 Sharing/Access information Data was derived from the following sources: *
 Versa 520 XRM (Zeiss, Pleasanton, CA, USA) running Scout and Scan software
 ## Software MATLAB scripts associated with the analysis of tomographic
 data including calculations of the solid volume fraction, covering radius
 transform, mean curvature, surface area, and Euler characteristic.