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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
Inproceedings Reference Shallow-water holothuroid (Echinodermata: Holothuroidea) biodiversity and biogeography of the subtropical coast of South Africa
see pdf
Located in Library / RBINS Staff Publications
Inproceedings Reference ROBOMINERS: changing the ground rules
Nowadays we are faced with several challenges regarding mineral exploration and exploitation in Europe. The biggest accessible deposits have already been discovered and exploited, with some of those mines dating back of thousands of years. What remains now are the small and difficult to access deposits, leading to the needs of new and more sustainable mining methods. In the last years several projects like ROBOMINERS were started with the expectation to have relevant impact in social, technological, environmental and economical areas and aiming to help in (i) reducing EU dependency on import of raw materials, (ii) pushing the EU to the forefront in sustainable minerals surveying and exploration technologies and to (iii) improve resource efficiency and responsible sourcing. The main objective of the ROBOMINERS project is to develop a Bio-Inspired, Modular and Reconfigurable Robot Miner, equipped with selective mining perception and mining tools for small and difficult to access deposits. A consortium that includes geoscientists, roboticists and engineers is working to build a modular robot prototype (Technology Readiness Level 4 to 5), design a new mining system via simulation and modelling and to use the prototype to study and advance future research on different areas of robotics and raw materials alike (Lopez and al. 2020). ROBOMINERS will not reach its end-state by the end of the project. Therefore, it already prepares future development with visions for 2030 and 2050, coinciding with important EU targets (2030: reduce GHG emissions, more renewable energy; 2050: climate neutrality). These visions will impact the developments of robotics, selective mining and mining ecosystem. The considered methods and tools, although innovative at this point, will be continuously assessed, and compared to new technology developments in the relevant fields. The ROBOMINERS project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 820971. References. L. Lopes, B. Bodo, C. Rossi, S. Henley, G. Žibret, A. Kot-Niewiadomska, V. Correia, ROBOMINERS – Developing a bio-inspired modular robot-miner for difficult to access mineral deposits, Advances in Geosciences, Volume 54, 2020, 99–108
Located in Library / RBINS Staff Publications 2021
Inproceedings Reference Mineralogical and geochemical insights of Fe-Ti-P-REE mineralization in alkaline igneous complexes: example from the Kodal deposit, Oslo Rift, Norway
Located in Library / RBINS Staff Publications 2023
Inproceedings Reference A 1500 years-record of North Atlantic storminess from the Shetland Islands (UK) – preliminary insights
Located in Library / RBINS Staff Publications 2021
Inproceedings Reference Metagenomics of tsunami deposits: developments and challenges from a case study on the Shetland Islands (UK)
Located in Library / RBINS Staff Publications 2021
Inproceedings Reference Cranial morphology of Khirtharia inflata (Raoellidae, Artiodactyla)
Raoellidae are extinct small-sized semiaquatic artiodactyls that are the closest relatives to crown clade Cetacea. They display morphological features showing the transition between terrestrial and aquatic lifestyles and therefore bring crucial information to understand the earliest steps of cetacean evolution. Raoellid cranial morphology, including the ear region and endocranial morphology, has been documented using cranial remains referred to Indohyus indirae from the Kalakot area, Jammu and Kashmir in India. The study of these specimens highlighted that several cetacean features are already present in raoellids. The previously available Indohyus material was very deformed, preventing access to quantitative data and leading to potential misinterpretations. We describe new undeformed cranial material from the Kalakot area, documenting another raoellid species, Khirtharia inflata. The new observations allow us to complete our knowledge of raoellid cranial morphology, including the original shape of the cranium and brain endocast and to confirm the specificities of raoellid morphology within Artiodactyla. We further provide the first quantitative data for the different brain components and show that Raoellidae had low encephalization and neocorticalization values, much lower than cetaceans and close to early diverging, primitive, dichobunoid artiodactyls. Reconstruction of the blood sinuses above the cerebellum supports the previous “intraosseous” hypothesis about the initial steps of the development of the caudal venous rete mirabile in cetaceans. The presence of several cetacean cranial features in Raoellidae, such as the peculiar shape of the frontal, the strong postorbital constriction, the periotic involucrum, or the elongation of the olfactory bulbs, questions the definition of the Cetacea clade.
Located in Library / RBINS Staff Publications 2023 OA
Inproceedings Reference Influence of an urbanization gradient on the vertical stratification of arboreal ants in green areas
EVALUATION OF DIFFERENT TAXONOMIC LEVELS AS SURROGATES OF ANT DIVERSITY IN GREEN AREAS IN AN URBANIZED ENVIRONMENT E. B. A. KOCH1, T. S. MELO2,3,4, A. R. S. ANDRADE2,3, M. LEPONCE5 & J. H. C. DELABIE2,4 1Programa de Pós-graduação em Ecologia e Evolução, Universidade Estadual de Feira de Santana (UEFS), CEP: 44.036-900 - Feira de Santana, Bahia, Brazil, e-mail: elmoborges@gmail.com; 2Programa de Pós-graduação em Ecologia, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil; 3Centro de Ecologia e Conservação Animal, Universidade Católica do Salvador (UCSal), Salvador, Bahia, Brazil; 4Laboratório de Mirmecologia, Convênio Universidade Estadual de Santa Cruz (UESC)/Comissão Executiva do Plano da Lavoura Cacaueira (CEPLAC), Ilhéus, Bahia, Brazil; 5Biodiversity Monitoring & Assessment, Royal Belgian Institute of Natural Sciences (RBINS), Bruxelas, Belgium. In cities located in environments of high biological importance, urbanization leads to changes in biotic diversity, while monitoring these changes can be difficult. Studies have pointed to the use of metrics that replace species as an alternative. Surrogate models are easily determined measures of biodiversity that correlate strongly with species richness and with what you want to investigate, being useful for detecting or monitoring environmental changes. The use of higher taxonomic levels has been applied to groups of megadiverse organisms, such as arthropods, since difficulties in identifying species are predictable. The aim of this study was to evaluate the practicality of using taxonomic diversity of ants as a surrogate of green area coverage in an urban environment. Four levels of "surrogate resolutions" (subfamily, genus, indicator taxa, and intermediate resolution) were assessed to the taxonomic diversity of ants across three levels of urban green areas (Small = 0 to 35%
Located in Library / RBINS Staff Publications 2023
Inproceedings Reference Importance of green area rate nesting site and exotic species on native ants in an urban environment
EVALUATION OF DIFFERENT TAXONOMIC LEVELS AS SURROGATES OF ANT DIVERSITY IN GREEN AREAS IN AN URBANIZED ENVIRONMENT E. B. A. KOCH1, T. S. MELO2,3,4, A. R. S. ANDRADE2,3, M. LEPONCE5 & J. H. C. DELABIE2,4 1Programa de Pós-graduação em Ecologia e Evolução, Universidade Estadual de Feira de Santana (UEFS), CEP: 44.036-900 - Feira de Santana, Bahia, Brazil, e-mail: elmoborges@gmail.com; 2Programa de Pós-graduação em Ecologia, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil; 3Centro de Ecologia e Conservação Animal, Universidade Católica do Salvador (UCSal), Salvador, Bahia, Brazil; 4Laboratório de Mirmecologia, Convênio Universidade Estadual de Santa Cruz (UESC)/Comissão Executiva do Plano da Lavoura Cacaueira (CEPLAC), Ilhéus, Bahia, Brazil; 5Biodiversity Monitoring & Assessment, Royal Belgian Institute of Natural Sciences (RBINS), Bruxelas, Belgium. In cities located in environments of high biological importance, urbanization leads to changes in biotic diversity, while monitoring these changes can be difficult. Studies have pointed to the use of metrics that replace species as an alternative. Surrogate models are easily determined measures of biodiversity that correlate strongly with species richness and with what you want to investigate, being useful for detecting or monitoring environmental changes. The use of higher taxonomic levels has been applied to groups of megadiverse organisms, such as arthropods, since difficulties in identifying species are predictable. The aim of this study was to evaluate the practicality of using taxonomic diversity of ants as a surrogate of green area coverage in an urban environment. Four levels of "surrogate resolutions" (subfamily, genus, indicator taxa, and intermediate resolution) were assessed to the taxonomic diversity of ants across three levels of urban green areas (Small = 0 to 35%
Located in Library / RBINS Staff Publications 2023
Inproceedings Reference Evaluation of different taxonomic levels as surrogates of ant diversity in green areas in an urbanized environment
EVALUATION OF DIFFERENT TAXONOMIC LEVELS AS SURROGATES OF ANT DIVERSITY IN GREEN AREAS IN AN URBANIZED ENVIRONMENT E. B. A. KOCH1, T. S. MELO2,3,4, A. R. S. ANDRADE2,3, M. LEPONCE5 & J. H. C. DELABIE2,4 1Programa de Pós-graduação em Ecologia e Evolução, Universidade Estadual de Feira de Santana (UEFS), CEP: 44.036-900 - Feira de Santana, Bahia, Brazil, e-mail: elmoborges@gmail.com; 2Programa de Pós-graduação em Ecologia, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil; 3Centro de Ecologia e Conservação Animal, Universidade Católica do Salvador (UCSal), Salvador, Bahia, Brazil; 4Laboratório de Mirmecologia, Convênio Universidade Estadual de Santa Cruz (UESC)/Comissão Executiva do Plano da Lavoura Cacaueira (CEPLAC), Ilhéus, Bahia, Brazil; 5Biodiversity Monitoring & Assessment, Royal Belgian Institute of Natural Sciences (RBINS), Bruxelas, Belgium. In cities located in environments of high biological importance, urbanization leads to changes in biotic diversity, while monitoring these changes can be difficult. Studies have pointed to the use of metrics that replace species as an alternative. Surrogate models are easily determined measures of biodiversity that correlate strongly with species richness and with what you want to investigate, being useful for detecting or monitoring environmental changes. The use of higher taxonomic levels has been applied to groups of megadiverse organisms, such as arthropods, since difficulties in identifying species are predictable. The aim of this study was to evaluate the practicality of using taxonomic diversity of ants as a surrogate of green area coverage in an urban environment. Four levels of "surrogate resolutions" (subfamily, genus, indicator taxa, and intermediate resolution) were assessed to the taxonomic diversity of ants across three levels of urban green areas (Small = 0 to 35%
Located in Library / RBINS Staff Publications 2023