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Inproceedings Reference 3D imaging showdown: A Comparative Study of high-resolution 3D Imaging Techniques for Museum Collections
Located in Library / RBINS Staff Publications 2025
Inproceedings Reference Toward a Unified Platform for the Digital Twins of the Specimens of Natural History Collections
The digitization of natural history collections is revolutionizing the preservation and utilization of biological and geological specimens. These collections, encompassing diverse ecosystems and time periods, are invaluable for scientific research, education, and conservation. However, physical specimens face challenges such as degradation, limited accessibility, and logistical difficulties. Digitization addresses these issues by converting specimens into high-resolution digital formats, preserving their integrity and making them widely accessible. This presentation explores the development of a unified platform for the digital twins of natural history specimens, focusing on standardization, management, and accessibility of multimedia files. The platform aims to integrate various digitization efforts as the Distributed System of Scientific Collections (DiSSCo ERIC) in Europe. This initiative adheres to the FAIR principles (Findable, Accessible, Interoperable, and Reusable) to enhance research capabilities and interdisciplinary studies. Key components of the platform include: 1. Digitization Techniques: High-resolution imaging, 3D scanning, and photogrammetry are used to create digital twins of specimens. These techniques ensure comprehensive documentation and accessibility for scientific research. 2. Metadata: The Darwin Core and ABCD standards for biodiversity data are managed by the institution CMS and DICOM is used for high-resolution and 3D imaging data. Links between CMS and Multimedia server are achieved using UUID/permalinks. This ensures quality, consistency, and interoperability of data. 3. Multimedia File Management: The platform utilizes the Open Source ORTHANC server, which supports various multimedia formats and provides a RESTful API for integration with other systems. Custom plugins and viewers were adapted or developed to enhance the visualization and analysis of digital specimens. 4. Interdisciplinary Collaboration: By providing a unified structure, the platform facilitates large-scale data analysis including access by AI and fosters collaboration among researchers, educators, and the general public. The integration of digital technologies into natural history collections not only safeguards specimens but also democratizes access to data, enabling global research and education. The proposed platform represents a significant advancement in the field, promoting the preservation and utilization of natural history collections in the digital age using Open Sources technologies. The proposed platform can easily be reused in a CH context.
Located in Library / RBINS Staff Publications 2025
Inproceedings Reference Holocene stratigraphy of the shallow offshore zones of the Shetland Islands: Insights into paleotsunami and paleoenvironment reconstructions.
Located in Library / RBINS Staff Publications 2024
Inproceedings Reference Erste Ergebnisse zu Untersuchungen an Sedimenten des Storegga-Tsunamis im Schelfbereich der Shetland-Inseln (GB).
Located in Library / RBINS Staff Publications 2024
Inproceedings Reference Using modern associations of microfauna to improve local relative sea-level reconstructions – a local transfer function for the Shetland Islands (UK)
Located in Library / RBINS Staff Publications 2025
Inproceedings Reference Holocene stratigraphy of the shallow offshore zones of the Shetland Islands: Insights into paleotsunami and paleoenvironment reconstructions
Located in Library / RBINS Staff Publications 2025
Inproceedings Reference Biodiversity of the freshwater crabs of Benin (Potamonautidae): a genetic approach
Introduction: Published reports on freshwater crabs in Benin (West Africa) are very scarce and mention only two accepted taxa: Sudanonautes aubryi and S. monodi (the latter with no precise locality). The inventory of these species (described using specimens from Gabon and Cameroon, respectively) is still poorly known. Methods: Here, we explore the diversity of freshwater crabs in Benin using a selection of 18 specimens collected in 2022 and 2023 in a range of aquatic biotopes and throughout the country, except for the far north. The specimens were examined morphologically and sequenced for fragments of the COI, 16S and H3 genes. Results: Despite a general variability in color, shape, size and in the DNA sequences (proportion of substitution per site up to ca. 8% for COI, 3% for 16S and 0.3% for H3), our results suggest that all the Beninese crabs belong to a single species of the Sudanonautes genus. They also show that they are neither S. aubryi nor S. floweri, with which they show consistent morphological differences and larger proportions of substitution per site at COI (>10%), 16S (>6%) and H3 (>0.6%). Conclusions: The Beninese crabs may belong to an undescribed species. However, they are more likely conspecific with S. pelii, a species described from the coastal plain of Ghana, previously considered to be a junior synonym of S. aubryi, and whose lectotype’s photographs show no obvious morphological differences with the Sudanonautes crabs from Benin. It is therefore likely that S. pelii will have to be revalidated for certain populations of Sudanonautes crabs from Ghana, Benin and probably adjacent countries.
Located in Library / RBINS Staff Publications 2024
Unpublished Reference BIRDIE: A South Africa biodiversity data pipeline for wetlands and waterbirds. Decision making in the biodiversity sector is only as good as the data that underpins the science.
With ever-increasing pressure globally on freshwater resources and, in particular, on wetlands, there is an urgent need to monitor the status of these ecosystems. In this context, waterbirds often serve as flagship and indicator species for the wetland ecosystems which support them. The South Africa Biodiversity Data Pipeline for Wetlands and Waterbirds (the BIRDIE project, https://birdie.sanbi.org.za/), emerges from a collaboration between government, academia, and conservation NGOs, with the overarching objective of serving as a link between South African nation-wide waterbird data collection programmes and conservation managers, researchers and other stakeholders. A key objective of the project is to support South Africa’s reporting and implementation of Multilateral Environmental Agreements such as the Convention on Wetlands of International Importance (RAMSAR), the African-Eurasian Migratory Waterbirds Agreement (AEWA), and the Convention on Biological Diversity, in particular, contributing to Red-Listing assessments of waterbird species. <br /><br /> The project uses data from the Coordinated Waterbird Counts (CWAC) and the Southern African Bird Atlas Project (ABAP) to understand the distribution and population dynamics of waterbird species. These citizen-science data are processed with rigorous statistical analysis to gain insights about these processes that raw data might not reveal. CWAC collects abundance data for waterbird species at 688 wetland sites. Since 1992, counts have been done twice a year, in summer and winter, providing good long term records. This information is made available as reports and an interactive map component. This map viewer is also showing the ABAP occupancy models on 144 waterbird species for 16,220 geographical ‘pentads’. Since 2007, more than 17 million records have been collected for ABAP with about 2 million more being added each year. The project also aims to support site management and decision making and, in the future, we hope to see the BIRDIE project expand to other regions and integrate with other biodiversity portals to promote a better understanding of the interactions between different taxonomic groups associated with wetlands.
Located in Library / RBINS Staff Publications 2024
Inproceedings Reference H2020 Eurofleets+ Data Management: an integrated data stewardship approach across multidisciplinary Transnational Access cruises
In the scope of H2020 Eurofleets+ project, 28 Transnational Access cruises were funded to conduct multidisciplinary scientific research projects. In order to achieve Open data FAIRness, an integrated data management approach has been set up in synergy with the pan-European SeaDataNet infrastructure involving three NODCs as core partners. It resulted in the collection of a tremendous amount of data from which 66% had been preserved, more than 40% made Findable and 30% Interroperable. Achieving successful data management was allowed by a close collaboration and good communication between scientists and NODCs.
Located in Library / RBINS Staff Publications 2024
Inproceedings Reference Restoring nature's health: Investigating the effects of ecosystem restoration on zoonotic disease risk
Emerging infectious diseases (EIDs) pose a significant threat to global public health. Among the factors contributing to the increase of EIDs today, habitat degradation stands out as a prominent driver, exerting both direct and indirect influences on disease dynamics. While it is commonly assumed that simply reversing ecosystem degradation will restore disease regulation mechanisms, such a presumption may oversimplify the complex response involved. My PhD project aims to delve deeper into the mechanisms underlying the impact of ecosystem restoration on zoonotic disease risk by examining terrestrial small mammal (TSM) and microparasite diversity within sampling sites following a chronosequence of ecosystem restoration in the Congo Basin. Through comprehensive sampling methods, including the capture of TSMs, and collection of iDNA and acoustic samples, the project will investigate how small mammal and microparasite diversity and prevalence evolve over time post-restoration. An emphasis will be placed on a subset of vector-borne and directly transmitted microparasites associated with African TSMs frequently found in the Congo Basin (i.e. Hepaciviruses, Paramyxoviruses, Orthonairovirus, Leptospira, Bartonella, and Anaplasma). The findings of this study will help unravel the complex interactions between ecosystem restoration, biodiversity, and zoonotic disease risk, offering crucial insights for the improvement and safeguarding of human, animal, and ecosystem health. This research is situated within the framework of the RESTOREID project (Horizon Europe; PI: Herwig Leirs), which aims to investigate the role of landscape restoration in mitigating disease risk using various field sites in Europe and Africa.
Located in Library / RBINS Staff Publications 2025