A dataset comprising 141 magnetic resonance imaging scans of 98 extant sea urchin species

Abstract

BackgroundApart from its application in human diagnostics, magnetic resonance imaging (MRI) can also be used to study the internal anatomy of zoological specimens. As a non-invasive imaging technique, MRI has several advantages, such as rapid data acquisition, output of true three-dimensional imagery, and provision of digital data right from the onset of a study. Of particular importance for comparative zoological studies is the capacity of MRI to conduct high-throughput analyses of multiple specimens. In this study, MRI was applied to systematically document the internal anatomy of 98 representative species of sea urchins (Echinodermata: Echinoidea).FindingsThe dataset includes raw and derived image data from 141 MRI scans. Most of the whole sea urchin specimens analyzed were obtained from museum collections. The attained scan resolutions permit differentiation of various internal organs, including the digestive tract, reproductive system, coelomic compartments, and lantern musculature. All data deposited in the GigaDB repository can be accessed using open source software. Potential uses of the dataset include interactive exploration of sea urchin anatomy, morphometric and volumetric analyses of internal organs observed in their natural context, as well as correlation of hard and soft tissue structures.ConclusionsThe dataset covers a broad taxonomical and morphological spectrum of the Echinoidea, focusing on ‘regular’ sea urchin taxa. The deposited files significantly expand the amount of morphological data on echinoids that are electronically available. The approach chosen here can be extended to various other vertebrate and invertebrate taxa. We argue that publicly available digital anatomical and morphological data gathered during experiments involving non-invasive imaging techniques constitute one of the prerequisites for future large-scale genotype—phenotype correlations.

Quantitative Classification of Cerebellar Foliation in Cartilaginous Fishes (Class: Chondrichthyes) Using Three-Dimensional Shape Analysis and Its Implications for Evolutionary Biology

“…Corfield et al, 2008a; Berquist et al, 2012; Zeigler et al, 2014]. Recent studies have demonstrated the utility of MRI for comparative brain morphology in marine mammals [Marino et al, 2001a, b; Montie et al, 2008; Oelschlager et al, 2010; Berns et al, 2015], birds [Corfield et al, 2008a, b], reptiles [Hoops et al, 2014], teleosts [Van der Linden et al, 2004; Ullmann et al, 2010a, b, c] and cartilaginous fishes [Pradel et al, 2009; Yopak et al, 2009, 2010a; Yopak and Frank, 2007], which provides invaluable data on the size and precise anatomical position of major neuroanatomical features and allows for the non-invasive assessment of specimens.…”

Schizasterid Heart Urchins Host Microorganisms in a Digestive Symbiosis of Mesozoic Origin

“…MRI data for one intact museum specimen each of A. cavernosus (27 mm TL) and A. cordatus (29 mm TL) previously obtained using a Pharmascan 70/16 MRI system (Bruker Biospin GmbH, Ettlingen, Germany) were integrated into the present study. Information on specimen preparation for MRI and scanning parameters has been published elsewhere ( Ziegler and Mueller, 2011 ; Ziegler et al, 2014 ).…”

Experiences in integrated data and research object publishing using GigaDB

“…This publication encouraged further submissions and publications from this community, such as 141 magnetic resonance imaging scans of 98 extant sea urchin species [96], three high-resolution microCT scans of brooding brittle stars [40], as well as a coordinated publication with journal, PLOS One [22], publishing the nearly 40GB of microCT data supporting a paper describing, in high resolution and 3D, the morphological features commonly used in earthworm taxonomy [41]. Despite some of the folders being close to 10GB in size, the data reviewers were able to retrieve each of those in as little as half an hour using our high-speed Aspera internet connection.…”