Societies rely on a secure, responsible and affordable supply of resources to meet their basic needs, in order to live life in a safe and healthy environment. The natural resources from the subsurface, i.e. groundwater, geo-energy and raw materials, represent essential elements in this provision. Safety from catastrophic events, such as those linked to earthquakes, or continuous ones, such as subsidence, can be improved by understanding the causes, frequency or rates of processes, and their impacts. These applied goals require a correct and intimate understanding of the regional geology. While geological surveys and other organisations working on the subsurface were initially very much focussed on national supply of resources, issues such as environmental consequences have increasingly come to the forefront. Europe has now become the relevant scale when considering import or export of raw materials. This results in an increasing pressure to place regional knowledge in a cross-border or pan-European context. To support cross-border, thematic research, the European Commission issued a call for an ERA-NET to which a consortium of 33 national and 15 regional organisations responded. An ERA-NET is a project that internally organises a competitive call for projects. In 2017, GeoERA officially started. After an internal call for project proposals, 15 projects were approved that receive about 30% top-up funding under H2020. The remainder of the resources comes from different sources of funding, totalling the budget to 30.3 M€. Projects are funded under the themes Geo-Energy, Raw Materials, and Ground Water. A fourth theme, Data Infrastructure, will realise the shared ambition of all projects to jointly store and publish their data on-line as an extension of country specific databases (e.g. DOV, Gisel). The starting date of the GeoERA research projects granted funding is 1 July 2018, and the projects will run for three years. Belgian and Flemish institutes involved are: the Geological Survey of Belgium (GSB), the Bureau for Environment and Spatial Development – Flanders (VPO), the Flemish Institute for Technological Research (VITO), Flanders Environment Agency (VMM) and the Belgian Nuclear Research Centre (SCK-CEN). Although not involved as official partner, the Geological Survey of Wallonia supports the initiative by means of data provision. The GSB is involved in seven projects, VITO, as linked third partyof VPO in two projects, VPO itself in one project, and VMM in three projects of which two will be elaborated in close cooperation with SCK-CEN, the linked third party of VMM. Together with VPO-VITO, the GSB is coordinator of GeoConnect³d, a strongly crossthematic Geo-Energy project that aims to disclose geological information for policy support and subsurface management. Other funded Geo-Energy projects in which the GSB is involved are MUSE, a project on shallow geothermal energy in European urban areas, and HIKE, on induced hazards and impacts related to the exploitation of subsurface resources throughout Europe. Under the theme Raw Materials the GSB participates in Mintell4EU, which aims to improve the European knowledge base on raw materials, as well as in FRAME, that is designed to research the critical and strategic raw materials in Europe. For groundwater the GSBeis directly involved in the HOVER project, mainly on data collection related to natural springs. VMM is also involved in HOVER, but in a work package on the distinction between anthropogenic and geogenic causes of groundwater contamination (especially how to deal with it in groundwater policy and management) with substances like arsenic. Moreover, VMM is, together with SCK-CEN, participating and leading a work package in two other Ground Water projects, namely VoGERA on investigating the vulnerability of shallow groundwater resources to deep subsurface energy-related activities, and RESOURces about harmonization of information about Europe’s groundwater resources through cross-border demonstration projects. Finally, the GIP-P project, where the GSB is work package leader, will establish a common platform for organising, disseminating and sustaining the digital results of the GeoERA projects. GeoERA is more than the occasional H2020 project. The combined efforts by the Belgian and Flemish institutes to engage in 10 different projects is a cooperative approach, with clear ambitions to demonstrate how cross-thematic research links can be set-up by different institutes, and how these can provide fruitful results for policy makers and other stakeholders. This is a notable effort in a project that is about establishing and demonstrating the added value of a European geological surveys research area, and finding how to optimally link regional, national and European efforts and interests. Acknowledgements This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No 731166
Located in
Library
/
RBINS Staff Publications 2018
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