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Inproceedings Reference Ways forward in quantifying data uncertainty in geological databases
Issues of compatibility of geological data resulting from the merging of many different data sources and time periods may jeopardize harmonization of data products. Important progress has been made due to increasing data standardization, e.g., at a European scale through the SeaDataNet and Geo-Seas data management infrastructures. Common geological data standards are unambiguously defined, avoiding semantic overlap in geological data and associated metadata. Quality flagging is also applied increasingly, though ways in further propagating this information in data products is still at its infancy. For the Belgian and southern Netherlands part of the North Sea, databases are now rigorously re-analyzed in view of quantifying quality flags in terms of uncertainty to be propagated through a 3D voxel model of the subsurface ( An approach is worked out to consistently account for differences in positioning, sampling gear, analysis procedures and vintage. The flag scaling is used in the interpolation process of geological data, but will also be used when visualizing the suitability of geological resources in a decision support system. Expert knowledge is systematically revisited as to avoid totally inappropriate use of the flag scaling process. The quality flagging is also important when communicating results to end-users. Therefore, an open data policy in combination with several processing tools will be at the heart of a new Belgian geological data portal as a platform for knowledge building (KB) and knowledge management (KM) serving the marine geoscience, the policy community and the public at large.
Located in Library / RBINS Staff Publications 2017
Article Reference Weak population structure and recent demographic expansion of the monogenean parasite Kapentagyrus spp. infecting clupeid fishes of Lake Tanganyika, East Africa
Located in Library / RBINS Staff Publications 2020
Article Reference Were ancient foxes far more carnivorous than recent ones? Carnassial morphological evidence
Crown shape variation of the first lower molar in the arctic (Vulpes lagopus) and red foxes (Vulpes vulpes) was analyzed using five groups of morphotypes. Carnassial morphologies were compared between the species and between spatially and temporally distant populations: one Late Pleistocene (n = 45) and seven modern populations of the arctic fox (n = 259), and one Late Pleistocene (n = 35) and eight modern populations of the red fox (n = 606). The dentition of Holocene red foxes had larger morphotype variability than that of arctic foxes. The lower carnassials of the red fox kept have some primitive characters (additional cusps and stylids, complex shape of transverse cristid), whereas the first lower molars of the arctic fox have undergone crown shape simplification, with the occlusal part of the tooth undergoing a more pronounced adaptation to a more carnivorous diet. From the Late Pleistocene of Belgium to the present days, the arctic fox’s crown shape has been simplified and some primitive characters have disappeared. In the red fox chronological changes in the morphology of the lower carnassials were not clearly identified. The phyletic tree based on morphotype carnassial characteristics indicated the distinctiveness of both foxes: in the arctic fox line, the ancient population from Belgium and recent Greenland made separate branches, whereas in the red foxes the ancient population from Belgium was most similar to modern red foxes from Belgium and Italy.
Located in Library / RBINS Staff Publications 2020
Inproceedings Reference What lies beneath the busiest shipping lane of the world? Stony reefs in the Belgian Continental Shelf: a quantitative mapping approach.
Located in Library / RBINS Staff Publications 2021 OA
Inproceedings Reference What's going on in (published) cave science? in press
Located in Library / RBINS Staff Publications 2021
Article Reference Where ichthyofaunal provinces meet: the fish fauna of the Lake Edward system, East Africa
Located in Library / RBINS Staff Publications 2019
Article Reference Whole-genome shotgun sequencing of mitochondria from ancient hair shafts
Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.
Located in Library / RBINS Staff Publications
Techreport Reference Working Group on Fisheries Benthic Impact and Trade-offs (WGFBIT; outputs from 2021 meeting).
Located in Library / RBINS Staff Publications 2022 OA
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 ( and RMCA ( 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
Techreport Reference Zeespiegelstijging voor Vlaanderen.
Located in Library / RBINS Staff Publications 2022 OA