Bringing collections out of the dark

Smith, Vincent; Blagoderov, Vladimir

doi:10.3897/zookeys.209.3699

Cited by 50 publications

(21 citation statements)

References 22 publications

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“…The development of standards and protocols for archiving and disseminating three-dimensional data as well as the creation of centralised registers to make the information retrievable remains an immediate priority (Ziegler et al 2010, Rowe and Frank 2011) and is crucial for the future success of these developments. In this context, natural history museums and other large natural collections will have to play a central role, not only by digitising their collections and thus massively producing data (as already exemplified by recent efforts (Smith and Blagoderov 2012)), but also by taking the lead in the development of standards and software for virtual museum collections and curation of cybertypes (for a discussion on the lack of standard file formats for interchange see Sutton et al 2012). This leads to another important issue—the current lack of standards to properly document and exchange volumetric data.…”

Section: Discussionmentioning

confidence: 99%

“…Godfray (2007) has argued that a possible solution to overcoming this bottleneck could be a web-based taxonomy using “cybertypes”, “based on the very best current imaging methods” (Godfray 2007), an idea immediately criticised by others (e.g Carvalho et al 2007). The idea of creating virtual collections of taxonomic material is, however, indeed enticing, and first implementations of accurate imaging methods, mass digitisations and remote access to digital material have been recently presented in a dedicated collection of papers (Smith and Blagoderov 2012, and references therein). Technological advances and a new generation of imaging techniques will inevitably open new horizons not only by providing rapid access to first-hand morphological information but also by making this information accessible to humans and computers alike.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Micro-computed tomography: Introducing new dimensions to taxonomy

Faulwetter¹,

Vasileiadou²,

Kouratoras³

et al. 2013

184

217

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Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowing rapid and simultaneous access to accurate virtual representations of type material. This paper explores the potential of micro-computed tomography (X-ray micro-tomography), a non-destructive three-dimensional imaging technique based on mapping X-ray attenuation in the scanned object, for supporting research in systematics and taxonomy. The subsequent use of these data as virtual type material, so-called “cybertypes”, and the creation of virtual collections lie at the core of this potential. Sample preparation, image acquisition, data processing and presentation of results are demonstrated using polychaetes (bristle worms), a representative taxon of macro-invertebrates, as a study object. Effects of the technique on the morphological, anatomical and molecular identity of the specimens are investigated. The paper evaluates the results and discusses the potential and the limitations of the technique for creating cybertypes. It also discusses the challenges that the community might face to establish virtual collections. Potential future applications of three-dimensional information in taxonomic research are outlined, including an outlook to new ways of producing, disseminating and publishing taxonomic information.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Micro-computed tomography: Introducing new dimensions to taxonomy

Faulwetter¹,

Vasileiadou²,

Kouratoras³

et al. 2013

184

217

View full text Add to dashboard Cite

show abstract

“…The digitisation of natural history collections is rapidly advancing (Blagoderov and Smith 2012), and natural history museums have a responsibility to not only create such cyberspecimens but also to take responsibility in curating and disseminating them. To make specimens continuously and simultaneously available to the research community, virtual collections such as those in the Micro-CTvlab will need to be deployed more massively, and these virtual collections will need to comprise mechanisms for an extensive documentation of the cyberspecimens so that they are searchable and retrievable (Faulwetter et al 2013, Stoev et al 2013).…”

Section: Additional Informationmentioning

confidence: 99%

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

Keklikoglou¹,

Faulwetter²,

Chatzinikolaou³

et al. 2016

BDJ

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BackgroundDuring recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create sub-micron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CTvlab) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro-CT data exploration of natural history specimens freely available over the internet.New informationThe Micro-CTvlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CTvlab can be accessed either on a normal computer or through a dedicated version for mobile devices.

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“…Digitisation of collections (databasing of label information and imaging) is a recent trend in herbarium management (Flannery, 2012). Public access to such information via the Internet makes collections more broadly useful and improves scientific research (Smith & Blagoderov, 2012).…”

mentioning

confidence: 99%