Reid M et al. (2019), A micro X-ray computed tomography dataset of fo...

ECB-ART-49952

Gigascience 2019 Mar 01;83:. doi: 10.1093/gigascience/giy156.

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A micro X-ray computed tomography dataset of fossil echinoderms in an ancient obrution bed: a robust method for taphonomic and palaeoecologic analyses.

Reid M , Bordy EM , Taylor WL , le Roux SG , du Plessis A .

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BACKGROUND: Taphonomic and palaeoecologic studies of obrution beds often employ conventional methods of investigation such as physical removal and extraction of fossils from their host rock (matrix) by mechanical preparation. This often-destructive method is not suitable for studying mold fossils, which are voids left in host rocks due to dissolution of the original organism in post-depositional processes. FINDINGS: Microcomputed tomography (µCT) scan data of 24 fossiliferous rock samples revealed thousands of Paleozoic echinoderms. Digitally "stitching" together individually µCT scanned rock samples within three-dimensional (3D) space allows for quantifiable taphonomic data on a fossil echinoderm-rich obrution deposit from the Devonian (Emsian) of South Africa. Here, we provide a brief step-by-step guide on creating, segmenting, and ultimately combining sections of richly fossiliferous beds to create virtual models suited for the quantitative and qualitative taphonomic analyses of fossil invertebrate assemblages. CONCLUSIONS: Visualizing the internal features of fossiliferous beds in 3D is an invaluable taphonomic tool for analyzing delicate fossils, accounting for all specimens irrespective of their preservation stages and with minimal damage. This technique is particularly useful for analyzing fossiliferous deposits with mold fossils that prove to be difficult to study with traditional methods, because the method relies on the large density contrast between the mold and host rock.

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	Figure 1. Karbonaatjies obrution bed that was excavated from Karbonaatjies farm (∼145 km northeast of Cape Town, South Africa). Each individual rock slab was given a reference letter in the field and subsequently reassembled in the lab.
	Figure 2. (A) Sample II, a long sample (26 cm x 12 cm) illustrating beam hardening artifacts causing the center of the sample to appear to have darker voxels while the edges appear much brighter, even though the sample is homogeneous. (B) Side view of sample II showing how the beam hardening artifact causes the pyrite minerals to give a "starburst" appearance. (C) Sample II after being cut and rescanned following the above-mentioned procedure.
	Figure 3. (A) Segmentation of ophiuroid specimens using the region growing tool in VGStudioMax. (B) The resulting virtually reconstructed ophiuroids in 3D, rendered with color and surrounding matrix set to transparent. (C) Reconstruction of a portion of the fossil bed in 3D (shaded area in Fig. 1). Black arrows point toward wax balls stuck to the upper surface of the samples to indicate right way up and relative positions.
	Figure 4. (A) Virtual reconstruction of samples SS, TT, TT2, TT3, and UU2 rendered with lights, color, and surrounding matrix set to 90% transparent. Approximately 80 articulated ophiuroids (light pink = ophiuroids oral side down; dark pink = ophiuroids oral side up), 13 paranacystids (green), 1 Placocystella (red) aulacophore fragment, numerous crinoid ossicles (blue), fragmented ophiuroid arms (pale orange), and large shell fragments (yellow) are all shown in 3D. (B) Side view shows three vaguely defined ophiuroid "horizons" as well as ophiuroid arms extended upward within the obrution bed.

References [+] :

Burrow, X-ray microtomography of 410 million-year-old optic capsules from placoderm fishes. 2005, Pubmed