Biodiversity exploration in the 3D era

Taxonomy – the discipline that defines and names groups of organisms – is a field of science that still employs many of the methods used during the beginnings of the discipline in the 18th century. Despite the increasing use of molecular information to delineate new species, the study of the morphology of specimens remains one of the major tasks of taxonomists. These studies often require first-hand examination of the reference specimens (so-called type material) deposited at museum collections around the globe - a time-consuming and laborious task.

To facilitate this procedure, a group of researchers from the Hellenic Centre for Marine Research (HCMR) are exploring the possibilities offered by 3D digital imaging. In a recent article published in the open-access journal ZooKeys, the researchers use X-ray computed tomography to create digital, three-dimensional representations of tiny animals, displaying both internal and external characteristics of the specimens at a detail level similar to that of the microscope.

To demonstrate their method, the researchers imaged a number of polychaete species (marine bristle-worms)—the choice of this group being obvious to Sarah Faulwetter, the leading author, because "despite being ecologically very important, these animals exhibit a fascinating diversity of forms and tissue types, allowing to test the methodology across a range of samples with different characteristics". The resulting interactive 3D models allow any researcher to virtually rotate, magnify or even dissect the specimen and thus extracting new scientific information, whereas the structure and genetic material of the analysed specimen are kept intact for future studies.

The team stress the importance of 3D imaging methods for taxonomy on its way into the twenty-first century: "Our vision for the future is to provide a digital representation of each museum specimen, simultaneously accessible via the internet by researchers and nature enthusiasts worldwide," says the team leader, Dr Christos Arvanitidis from HCMR. The instant accessibility of specimens will speed up the creation and dissemination of knowledge. As the authors point out, "human efforts, combined with novel technologies, will help taxonomy to turn into a cyberscience whose discoveries might rival those made during the great naturalist era of the nineteenth century."



See also the playlist in the Pensoft video channel.


The study was supported by the European Union projects MARBIGEN (FP7-REGPOT-2010-1) and ViBRANT (RI-261532)


Original Source: Faulwetter S, Vasileiadou A, Kouratoras M, Dailianis T, Arvanitidis C (2013) Micro-computed tomography: Introducing new dimensions to taxonomy. ZooKeys 263: 1-45. doi: 10.3897/zookeys.263.4261

MARBIGEN Researcher awarded with Encyclopedia of Life Rubenstein Fellowship


Washington, D.C. - January 28, 2013 - The Encyclopedia of Life (EOL) is pleased to announce the winners of the 2013 EOL Rubenstein Research Fellowship awards.  The seven awardees will lead research teams seeking to answer novel research questions not readily addressable without the extensive data resources served by EOL.  EOL Rubenstein Research Fellow awards are made possible by a generous gift to EOL by David M. Rubenstein through the Smithsonian Institution’s National Museum of Natural History.

Introductory course to the Principles of Coalescent Theory and Applications

Event Date: 
Mon, 2012-02-20 15:00 - Fri, 2012-02-24 18:00

The course is intended for students, researchers and/other academic personnel with minimal or no programming knowledge who wish to obtain a basic understanding Coalescent theory and its applications and hands-on experience in using R as a programming language applied to coalescent theory models. Courses are scheduled for the period of the 20th to the 24th of February 2012 and will take place from 15:00 to 18:00 at the seminar room of HCMR. The course will comprise five (5) 3-hour sessions (incl. theory and practicals). The topics that will be covered are:

Workshop on “Next Generation Sequencing technologies and informatics tools for studying marine biodiversity and adaptation”

Event Date: 
Mon, 2012-10-01 00:00 - Wed, 2012-10-03 00:00

IMBG – HCMR, Heraklion, Crete, Greece
Workshop official site:

Workshop: Genomics in Biodiversity

The workshop targeted mainly PhD students and post-docs, but also researchers interested in high-throughput DNA analysis methods were welcome. Basic knowledge in informatics was required but not mandatory. Through this workshop IMBG facilities promoted possible new collaborations. In addition, IMBG personnel had also the opportunity to follow lectures comprising new DNA analysis methods and their integration to applied research as lectures of top ranked institutes were invited to give lectures. Within this framework Dr.

"Microbial Diversity, Genomics and Metagenomics"

Event Date: 
Tue, 2011-12-13 00:00 - Fri, 2011-12-16 00:00

Workshop on "Microbial Diversity, Genomics and Metagenomics"

IMBG – HCMR, Heraklion, Crete, Greece
13 December – 16 December 2011

Introduction to Systems Biology: Gene networks, Metabolic networks, Protein Networks, The future of Biology

Event Date: 
Wed, 2011-11-16 09:00 - Sat, 2011-11-19 18:00

Introduction to Systems Biology
by Prof. Christos Ouzounis
Principal Investigator, CERTH Thessalonica, Greece &
Visiting Professor, The Terrence Donnelly Centre for Cellular
& Biomolecular Research (CCBR), University of Toronto, Canada


1. Thursday 17/11/2011
09:30 - 11:00 - Gene networks
12:00 - 13:30 - Metabolic networks

2. Friday 18/11/2011
09:30 - 11:00 - Protein Networks
12:00 - 13:30 - The future of Biology

Video gallery of MicroCT scans

A video gallery of organisms scanned with the SkyScan 1172 MicroCT is available at the MARBIGEN site.

The videos are also available in a 3D version, for which red-blue 3D glasses are needed.

MicroCT Seminar by SkyScan

From 11.-14. October 2011, Jeroen Hostens of SkyScan gave a 3-day training seminar on the usage of the SkyScan 1172 MicroCT scanner installed in the facilities of IMBG. The training covered the handling and staining of specimens, scanning parameters, reconstruction of 3D images, creation of 3D models and the analyis software.

Genomics in Biodiversity

Event Date: 
Fri, 2011-09-16 00:00 - 18:00

DNA sequencing and genotyping technologies are advancing very fast, with the development
of novel methodologies and machinery and the utilization of new types of molecular markers

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