A dataset describing brooding in three species of South African brittle stars, comprising seven high-resolution, micro X-ray computed tomography scans

Abstract

BackgroundBrooding brittle stars have a special mode of reproduction whereby they retain their eggs and juveniles inside respiratory body sacs called bursae. In the past, studying this phenomenon required disturbance of the sample by dissecting the adult. This caused irreversible damage and made the sample unsuitable for future studies. Micro X-ray computed tomography (μCT) is a promising technique, not only to visualise juveniles inside the bursae, but also to keep the sample intact and make the dataset of the scan available for future reference.FindingsSeven μCT scans of five freshly fixed (70 % ethanol) individuals, representing three differently sized brittle star species, provided adequate image quality to determine the numbers, sizes and postures of internally brooded young, as well as anatomy and morphology of adults. No staining agents were necessary to achieve high-resolution, high-contrast images, which permitted visualisations of both calcified and soft tissue. The raw data (projection and reconstruction images) are publicly available for download from GigaDB.ConclusionsBrittle stars of all sizes are suitable candidates for μCT imaging. This explicitly adds a new technique to the suite of tools available for studying the development of internally brooded young. The purpose of applying the technique was to visualise juveniles inside the adult, but because of the universally good quality of the dataset, the images can also be used for anatomical or comparative morphology-related studies of adult structures.

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.…”

“…This method being increasingly impractical if we wanted to send the hard disks on in the same manner to downstream users. Even datasets in the 100GB range have been challenging to get hold of from less-connected corners of the world, where a microCT imaging dataset from South Africa took one month to be copied to our servers due to bandwidth problems and regular power cuts at their university, requiring the process to be restarted a number of times [40]. Popular datasets require greater bandwidth, and the E. coli nanopore dataset mentioned above had to be mirrored in AWS S3 for the first month to cope with the huge short-term demand [64].…”

Micro-CTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT)

“…However, although many micro-CT datasets of biological specimens are being created and published (e.g. Lenihan et al 2014, Akkari et al 2015, Landschoff et al 2015, Tessler et al 2016), a standardised practice for metadata annotation or publication of such datasets is absent (Faulwetter et al 2013, Stoev et al 2013). The reasons for this are: a) micro-CT datasets typically are large (several GB per dataset), thus storage space and manpower for adequate curation need to be reserved; b) existing community standards for biodiversity data (e.g.…”

Sanguessugas parasitas da ordem Rhyncobdellida (Clitellata: Hirudinida) do território brasileiro

“…2016) e uma grande variedade de táxons já tiveram membros estudados a partir de técnicas de imagens tridimensionais, mas não cumprem os quesitos necessários para serem considerados cybertipos, conforme estabelecido por Faulwetter et al (2013) (ex. Fernández et al, 2014Landschoff et al, 2015;Steinhoff & Uhl, 2015). Estes autores estabeleceram que, para uma base de dados ser considerada como um cybertipo, esta deve cumprir pelo menos três principais critérios: (a) fornecer informações sobre a morfologia interna e externa com a mesma confiança e acurácia que os espécimes reais; (b) deve representar um espécime real que pertença ao material tipo; e (c) deve ter fácil acesso através de meios de publicação digitais (Faulwetter et al, 2013 (Metscher, 2009a, b).…”

“…Pelo menos dois cybertipos foram publicados nesta revista e estão disponíveis para consulta (Carbayo & Lenihan, 2016;Landschoff et al, 2015). Além das dificuldades inatas à técnica, durante o tratamento dos dados foram encontradas diversas dificuldades relacionadas ao tamanho e a quantidade de dados gerados, uma característica de qualquer base classificada como "Big Data" (Chen & Zhang, 2014).…”