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Inproceedings Reference X-ploring new tools for paleontologists: the RBINS-RMCA micro-CT lab at your service!
X-ray computed tomography (CT-) scanning is revolutionizing the study of extinct organisms. Its non-invasive and non-destructive character makes it currently by far the most potent method to allow fossils to be studied in three dimensions and with unprecedented detail. More importantly, and differing from other 3D techniques, CT-scanning looks through and inside objects, revealing hidden structures and characters. Recent innovations in the field of CT-scanning allow obtaining details up to a few micrometers in resolution, and higher quality images of relatively dense materials, like fossils, even when wholly encased in hard sediment (Keklikoglou et al., 2019). In 2016, the Royal Belgian Institute of Natural Sciences (RBINS) acquired two high-end X-ray CT machines: the micro-CT RX EasyTom and the nano-CT XRE-Tescan UniTom. Both scanners are currently nearly full time in use to help accomplishing the gigantic task of the digitization of the RBINS and Royal Museum for Central Africa (RMCA) type collections, the aim of two multi-year Belspo funded projects, DiSSCo-Fed (2018-2023) and DIGIT-4 (2019-2024). With about 300.000 types and 48.000.000 general specimens, 46.000 and 3.000.000 respectively in their paleontology collections, the results of nearly two centuries of intensive collecting and research, these two Belgian Federal Scientific Institutions (FSI’s) are major players in the European framework of scientific research infrastructures for natural history. Digitizing this large number of types, spread across almost the entire Tree of Life, and exhibiting an entire array of differing taphonomies, results in a steadily growing expertise of the RBINS-RMCA micro-CT lab (Brecko et al., 2018). While the newly acquired infrastructure and ongoing digitization projects are primarily oriented towards the digitization of type and figured specimens, these also offer great opportunities for researchers and teachers in various disciplines of paleontology. Targeting on researchers interested in incorporating micro-CT as a technique in their research projects, the current digitization workflow of the RBINS-RMCA micro-CT lab will be presented. While micro-CT offers many advantages, there are also pitfalls and limitations that need to be considered. Based on our expertise, and illustrated by some of our scanning results, important constraints that may block the pathway between your expectations and perfect micro-CT-imaging results that can be fully incorporated into research projects will be presented. Possible effects of some of the most important parameters that may influence the quality of the output, and thus can increase the signal to noise ratio (SNR) will be reviewed, such as the size and shape of the specimen to be scanned, the density of its matrix the specimen is made of or encased in, the presence of certain minerals (e.g. pyrite) and how these may be distributed inside the specimen (e.g. finely disseminated, dense masses or crystals), the best possible resolution in relation to the specimen and preferred output, the time needed to scan a specimen, the choice between machines to be used and their limits and different possible scan settings (e.g. beam power, filters…). Post-processing parameters to be considered are the size of the image stack output (will the computer be able to handle the amount of Gigabytes?), the time needed to render and segment regions of interest and optimize 3D-models, and which format suits best to visualize and export the data (renderings, meshes, videos, virtual sections…). While segmentation may be a time-consuming task, new developments like the incorporation of artificial intelligence (e.g. the Deep Learning function in Dragonfly ORS) offer great potential to reduce the workload in complex segmentation. Many researchers are also teachers. The reason why they may also be particularly interested in the 3D models of the already digitized types that are available on the Virtual Collections platforms of the RBINS (http://virtualcollections.naturalsciences.be/) and RMCA (https://virtualcol.africamuseum.be/). While 3D models are not intended to replace physical specimens, they may become significant teaching aids in both the physical and virtual classroom. In addition, the presence of a steadily growing number of 3D-models and animations of extant animals that are also added to these Virtual Collections, would allow teachers to connect fossils (in general incomplete) with extant (more complete) relatives. Last but not least, while the focus of this communication is largely on micro-CT, some of the many other new techniques that are being tested, used and improved will be highlighted (see e.g. Brecko & Mathys, 2020; Brecko et al., 2014, 2016, 2018; Mathys et al., 2013, 2019 for some examples). Interested in our work, expertise, techniques, equipment, or scans-on-demand? Please do not hesitate to reach out! References Brecko, J., Lefevre, U., Locatelli, C., Van de Gehuchte, E., Van Noten, K., Mathys, A., De Ceukelaire, M., Dekoninck, W., Folie, A., Pauwels, O., Samyn, Y., Meirte, D., Vandenspiegel, D. & Semal, P. 2018. Rediscovering the museum’s treasures: μCT digitisation of the type collection. Poster presented at 6th annual Tomography for Scientific Advancement (ToScA) symposium, Warwick, England, 10-12 Sept 2018. Brecko, J. & Mathys, A., 2020. Handbook of best practice and standards for 2D+ and 3D imaging of natural history collections. European Journal of Taxonomy, 623, 1-115. Brecko, J., Mathys, A., Dekoninck, W., De Ceukelaire, M., VandenSpiegel, D. & Semal, P., 2016. Revealing Invisible Beauty, Ultra Detailed: The Influence of Low-Cost UV Exposure on Natural History Specimens in 2D+ Digitization. PLoS One 11(8):e0161572. Brecko, J., Mathys, A., Dekoninck, W., Leponce, M., Vanden Spiegel, D. & Semal, P., 2014. Focus stacking: Comparing commercial top-end set-ups with a semi-automatic low budget approach. A possible solution for mass digitization of type specimens. Zookeys, 464, 1-23. Keklikoglou, K., Faulwetter, S., Chatzinikolaou, E., Wils, P., Brecko, J., Kvaček, J., Metscher, B. & Arvanitidis, C. 2019. Micro-computed tomography for natural history specimens: a handbook of best practice protocols. European Journal of Taxonomy, 522, 1-55. Mathys, A., Semal, P., Brecko, J. & Van den Spiegel, D., 2019. Improving 3D photogrammetry models through spectral imaging: Tooth enamel as a case study. PLoS One, 14(8): e0220949. Mathys, A., Brecko, J., Di Modica, K., Abrams, G., Bonjean, D. & Semal, P., 2013. Agora 3D. Low cost 3D imaging: a first look for field archaeology. Notae Praehistoricae, 33/2013, 33-42.
Located in Library / RBINS Staff Publications 2021
Article Reference Organic matter processing in a [simulated] offshore wind farm ecosystem in current and future climate and aquaculture scenarios
The rapid development of blue economy and human use of offshore space triggered the concept of co-location of ma- rine activities and is causing diverse local pressures on the environment. These pressures add to, and interact with, global challenges such as ocean acidification and warming. This study investigates the combined pressures of climate change and the planned co-location of offshore wind farm (OWF) and aquaculture zones on the carbon flow through epifaunal communities inhabiting wind turbines in the North Sea. A 13 C-labelled phytoplankton pulse-chase experi- ment was performed in mesocosms (4 m 3 ) holding undisturbed hard-substrate (HS) communities, natural sediment with infauna, and mobile invertebrate predators. Carbon assimilation was quantified under current and predicted future-climate conditions (+3 °C and −0.3 pH units), as well as a future-climate co-use scenario with blue mussel (Mytilus edulis) aquaculture. Climate change induced an increase in macrofaunal carbon assimilation as well as an organic enrichment of underlying sediments. Dynamic (non-)trophic links between M. edulis and other HS epifauna resulted in shifts among the species contributing most to the phytoplankton-derived carbon flow across climate scenar- ios. Increased inter- and intraspecific resource competition in the presence of M. edulis aquaculture prevented a large increase in the total assimilation of phytoplankton by HS fauna. Lower individual carbon assimilation rates by both mussels and other epifauna suggest that if filter capacity by HS epifauna would approach renewal by advection/ mixing, M. edulis individuals would likely grow to a smaller-than-desired commercial size. In the same scenario, ben- thic organic carbon mineralisation was significantly boosted due to increased organic matter deposition by the aqua- culture set-up. Combining these results with in situ OWF abundance data confirmed M. edulis as the most impactful OWF AHS species in terms of (total) carbon assimilation as well as the described stress responses due to climate change and the addition of bivalve aquaculture.
Located in Library / RBINS Staff Publications 2022
Inproceedings Reference Taxonomic and phylogenetic study of the late Oligocene heterodont odontocete Eosqualodon langewieschei provides clues about the emergence of modern toothed whales
Located in Library / RBINS Staff Publications 2022
Article Reference Revision of the lanternfly genus Limois Stål, 1863 (Hemiptera: Fulgoromorpha: Fulgoridae) with description of a new species from China
Located in Library / RBINS Staff Publications 2020
Inproceedings Reference Shallow-water holothuroid (Echinodermata: Holothuroidea) biodiversity and biogeography of the subtropical coast of South Africa
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Located in Library / RBINS Staff Publications
Article Reference Taxonomy of the monotypic genus Koehleria Cherbonnier, 1988 (Echinodermata: Holothuroidea: Cucumariidae)
Voucher material recently collected from the 2-Mile Reef at Sodwana Bay (Republic of South Africa), allows the evaluation of the monotypic genus Koehleria Cherbonnier, 1988 and its species K. unica Cherbonnier, 1988 collected from Tuléar (Madagascar). Cherbonnier’s (1988) conclusion, that Koehleria is most related to the also monotypic genus Pseudocolochirus Pearson, 1910 is correct, but the differences between Koehleria and Pseudocolochirus are too small to justify the retention of Koehleria. Koehleria is relegated herein to the synonymy of Pseudocolochirus. Such a step decreases the velocity with which monotypic genera are currently described within the Dendrochirotida.
Located in Library / No RBINS Staff publications
Article Reference Sea Cucumbers of the Comoros Archipelago
Sea cucumbers have been harvested for centuries in the Far East. Overexploitation, coupled with increasing demand has led to local depletion of certain standing stocks. De novo investigation at Grande Comore (one of the four main islands of the Comoros Archipelago) allows reappraisal of local holothuroid biodi- versity. Comparison with neighbouring areas allows extrapolation of holothuroid species richness to the rest of the archipelago. The current exploitation of holothuroids has been documented and there are definite signs of overexploitation. Conservation measures are urgently needed if exploitation of sea cucumbers in this area is to become sustainable in the near future.
Located in Library / RBINS Staff Publications
Article Reference A new species of Actinopyga (Holothuroidea: Aspidochirotida: Holothuriidae)
Actinopyga is one of the five genera commonly recognised in the family Holothuriidae. This small genus has sixteen species currently considered valid. The present paper describes a new Indo-West Pacific species, Actinopyga caerulea, of which the most striking character is its bluish coloration. The ossicle assemblage of the new species resembles mostly that of A. bannwarthi Panning, 1944 and A. flammea Cherbonnier, 1979.
Located in Library / RBINS Staff Publications
Article Reference Interdisciplinaire studie van tuinbouwactiviteiten: archeobotanisch, geoarcheologisch en archeozoölogisch onderzoek van de laatmiddeleeuwse zwarte lagen van de Kreupelenstraat/Zilverstraat (BHG/RBC)
Located in Library / RBINS Staff Publications 2020
Article Reference Brucity/Parking 58 : Un ancien quai de Senne (XVe siècle) (RBC/BHG)
Located in Library / RBINS Staff Publications 2020