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

Keklikoglou, Kleoniki; Faulwetter, Sarah; Chatzinikolaou, Eva; Michalakis, Nikitas; Filiopoulou, Irene; Minadakis, Nikos; Panteri, Emmanouela; Perantinos, George; Gougousis, Alexandros; Arvanitidis, Christos

doi:10.3897/bdj.4.e8740

Cited by 13 publications

(9 citation statements)

References 19 publications

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“…Another relevant aspect of the use of micro-CT, when considered as a virtual dissection technique, is that it allows for the examination of internal organs, in their natural anatomical context, without harming body integrity. Furthermore, by using appropriate software, the stack of data can be stored and shared with other scientists (see Keklikoglou et al, 2016), thus allowing for a far better and quicker dissemination and exchange of information.…”

Section: Discussionmentioning

confidence: 99%

An integrative approach to the anatomy of Syllis gracilis Grube, 1840 (Annelida) using micro-computed X-ray tomography

Parapar

Caramelo

Candás

et al. 2019

PeerJ

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Background The overall anatomy of the genus Syllis (Annelida: Syllidae) has been largely studied; however, an integrative approach considering different anatomical techniques has never been considered. Here, we use micro-computed X-ray tomography (micro-CT) to examine the internal anatomy of Syllis gracilis Grube, 1840, along with other widely available techniques. Methods We studied the anatomy of the marine annelid S. gracilis through an integrative approach, including micro-CT along with stereo and light compound microscopy (STM, LCM), scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM) and histological sectioning (HIS). In this manner, we evaluated the applicability of micro-CT for the examination of annelid anatomy by testing whether the images obtained make it possible to visualize the main body structures, in comparison with other current techniques, of the various elements of its internal anatomy. Results Overall external and internal body elements are clearly shown by the integrative use of all techniques, thus overcoming the limitations of each when studied separately.Any given method shows disparate results, depending on the body part considered. For instance, micro-CT provided good images of the external anatomy, including relevant characters such as the shape, length and number of articles of dorsal parapodial cirri. However, it is especially useful for the examination of internal anatomy, thus allowing for 3D visualization of the natural spatial arrangement of the different organs. The features best visualized are those of higher tissue density (i.e., body musculature, anterior parts of the digestive tract), particularly in 3D images of unstained specimens, whereas less electrodense tissues (i.e., the peritoneal lining of septa and nervous system) are less clearly visualized. The use of iodine stain with micro-CT has shown advantages against non-staining for the adequate observation of delicate elements of low density, such as the segmental organs, the connective between the ganglia, the ventral nerve cord and segmental nerves. Discussion Main external anatomical elements of S. gracilis are well shown with micro-CT, but images show lesser optical resolution and contrast when compared to micrographs provided by SEM and CLSM, especially for fine structural features of chaetae. Comparison of micro-CT and HIS images revealed the utility and reliability of the former to show the presence, shape and spatial disposition of most internal body organs; the resolution of micro-CT images at a cellular level is, however, much lower than that of HIS, which makes both techniques complementary.

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Section: Discussionmentioning

confidence: 99%

An integrative approach to the anatomy of Syllis gracilis Grube, 1840 (Annelida) using micro-computed X-ray tomography

Parapar

Caramelo

Candás

et al. 2019

PeerJ

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“…Furthermore, species records are connected to the Micro-CT vlab sub-application of LifeWatchGreece mobile app where users can explore relevant Micro-CT datasets (i.e. series of images using X-Ray micro-computed tomography) through images, videos and 3D models that can be virtually manipulated, dissected and rotated using online tools (see Keklikoglou et al 2016, this special collection).…”

Section: Resultsmentioning

confidence: 99%

CIGESMED for divers: Establishing a citizen science initiative for the mapping and monitoring of coralligenous assemblages in the Mediterranean Sea

Gerovasileiou¹,

Dailianis²,

Panteri³

et al. 2016

BDJ

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BackgroundOver the last decade, inventorying and monitoring of marine biodiversity has significantly benefited from the active engagement of volunteers. Although several Citizen Science projects concern tropical reef ecosystems worldwide, none of the existing initiatives has yet specifically focused on their Mediterranean equivalents. Mediterranean coralline reefs, known as “coralligenous”, are bioherms primarily built by calcifying rhodophytes on hard substrates under dim-light conditions; they are considered hotspots of biodiversity and are extremely popular among divers due to their complex structure, conspicuous biological wealth and high aesthetic value. Nevertheless, data on their distribution, structure and conservation status is lacking for several Mediterranean areas while they are vulnerable to an increasing number of threats.New informationIn the framework of CIGESMED SeasEra (ERAnet) project a specialized Citizen Science project was launched, aiming to engage enthusiast divers in the study and monitoring of Mediterranean coralligenous assemblages through the gathering of basic information regarding their spatial occurrence, assemblage structure and associated pressures or threats. For its active implementation, a data collection protocol and a multilingual website were developed, comprising an educational module and a data submission platform. Georeferenced data reporting focuses on: (a) basic topographic and abiotic features for the preliminary description of each site, and the creation of data series for sites receiving multiple visits; (b) presence and relative abundance of typical conspicuous species, as well as (c) existence of pressures and imminent threats, for the characterization and assessment of coralligenous assemblages. A variety of tools is provided to facilitate end users, while divers have the choice to report additional information and are encouraged to upload their photographs. The long-term goal is the development of an active community of amateur observers providing widespread and ecologically significant data on coralligenous assemblages.

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“…Digitised specimens, however, are available at the click of a mouse from any internet-enabled computer worldwide, protect the specimen from loss or damage through handling or shipping and thus have the potential to accelerate taxonomic and systematic research and allow for large-scale comparative morphological studies (Faulwetter et al 2013a). Micro-CT imaging technology may give rise to the elaboration of 'virtual museums' or 'virtual laboratories' where digital data are shared widely and freely around the world, while the original material is stored safely (Abel et al 2011;Keklikoglou et al 2016). In addition, 3D models created through micro-CT scanning can be either printed or made available via interactive touch screens to be used for public display and outreach efforts.…”

Section: Scope and Structure Of This Handbookmentioning

confidence: 99%

Micro-computed tomography for natural history specimens: a handbook of best practice protocols

Keklikoglou

Faulwetter

Chatzinikolaou

et al. 2019

EJT

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Micro-computed tomography (micro-CT or microtomography) is a non-destructive imaging technique using X-rays which allows the digitisation of an object in three dimensions. The ability of micro-CT imaging to visualise both internal and external features of an object, without destroying the specimen, makes the technique ideal for the digitisation of valuable natural history collections. This handbook serves as a comprehensive guide to laboratory micro-CT imaging of different types of natural history specimens, including zoological, botanical, palaeontological and geological samples. The basic principles of the micro-CT technology are presented, as well as protocols, tips and tricks and use cases for each type of natural history specimen. Finally, data management protocols and a comprehensive list of institutions with micro-CT facilities, micro-CT manufacturers and relative software are included.

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

Cited by 13 publications

References 19 publications

An integrative approach to the anatomy of Syllis gracilis Grube, 1840 (Annelida) using micro-computed X-ray tomography

An integrative approach to the anatomy of Syllis gracilis Grube, 1840 (Annelida) using micro-computed X-ray tomography

CIGESMED for divers: Establishing a citizen science initiative for the mapping and monitoring of coralligenous assemblages in the Mediterranean Sea

Micro-computed tomography for natural history specimens: a handbook of best practice protocols

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