The demand for the digitization of natural history collections has increased with the advancement of imaging technologies. Large collections composed of millions of insect specimens are exploring efficient strategies and new technologies to digitize them. However, many of these new systems are quite elaborate and expensive, creating a need for more affordable and easy-to-use equipment.
75-by-47-cm foam platform with pinned insects in dorsal and lateral positions.
Creating a digital image for every specimen is an essential part of the DNA barcoding workflow at the Centre for Biodiversity Genomics (CBG). A newly designed imaging rig has enabled the CBG to quickly and efficiently image specimens at high quality while controlling the specimen’s orientation to emphasize key morphological characters. This system allowed the CBG to take some 190,000 images over the past year.
The SLR rig is placed on a heavy-base table to minimize vibration. The inset shows the actual rig area with specimens on the styrofoam base.
Our new ZooKeys study describes this imaging rig, which was mainly created for pinned specimens. It is inexpensive and easy to install as it uses a camera mounted to a CNC machine rig to photograph specimens at high capacity. By using a foam board to array specimens, the user can choose their orientation, which contrasts some existing methods that do not provide such flexibility. This setup produces 95 high quality images within half an hour.
Panel of example images taken with the SLR rig.
The flexibility of the imaging rig could benefit many potential users who are looking for an accessible method for larger collections of specimens. By alternating various parameters, such as the distance between the camera and specimens or the type of camera and lens used, users can adapt their system to specimens of varying sizes. With further changes to the array, the imaging rig can also be adapted to support imaging specimens on slides, within vials, or other storage solutions.
Leiden – also known as the ‘City of Keys’ and the ‘City of Discoveries’ – was aptly chosen to host the third Empowering Biodiversity Research (EBR III) conference. The two-day conference – this time focusing on the utilisation of biodiversity data as a vehicle for biodiversity research to reach to Policy – was held in a no less fitting locality: the Naturalis Biodiversity Center.
On 25th and 26th March 2024, the delegates got the chance to learn more about the latest discoveries, trends and innovations from scientists, as well as various stakeholders, including representatives of policy-making bodies, research institutions and infrastructures. The conference also ran a poster session and a Biodiversity Informatics market, where scientists, research teams, project consortia, and providers of biodiversity research-related services and tools could showcase their work and meet like-minded professionals.
BiCIKL stops at the Naturalis Biodiversity Center
The main outcome of the BiCIKL project: the Biodiversity Knowledge Hub, a one-stop knowledge portal to interlinked and machine-readable FAIR data.
The famous for its bicycle friendliness country also made a suitable stop for BiCIKL (an acronym for the Biodiversity Community Integrated Knowledge Library): a project funded under the European Commission’s Horizon 2020 programme that aimed at triggering a culture change in the way users access, (re)use, publish and share biodiversity data. To do this, the BiCIKL consortium set off on a 3-year journey to build on the existing biodiversity data infrastructures, workflows, standards and the linkages between them.
Many of the people who have been involved in the project over the last three years could be seen all around the beautiful venue. Above all, Naturalis is itself one of the partnering institutions at BiCIKL. Then, on Tuesday, on behalf of the BiCIKL consortium and the project’s coordinator: the scientific publisher and technology innovator: Pensoft, Iva Boyadzhieva presented the work done within the project one month ahead of its official conclusion at the end of April.
As she talked about the way the BiCIKL consortium took to traverse obstacles to wider use and adoption of FAIR and linked biodiversity data, she focused on BiCIKL’s main outcome: the Biodiversity Knowledge Hub (BKH).
Key results from the BiCIKL project three years into its existence presented by Pensoft’s Iva Boyadzhieva at the EBR III conference.
Intended to act as a knowledge broker for users who wish to navigate and access sources of open and FAIR biodiversity data, guidelines, tools and services, in practicality, the BKH is a one-stop portal for understanding the complex but increasingly interconnected landscape of biodiversity research infrastructures in Europe and beyond. It collates information, guidelines, recommendations and best practices in usage of FAIR and linked biodiversity data, as well as a continuously expanded catalogue of compliant relevant services and tools.
At the core of the BKH is the FAIR Data Place (FDP), where users can familiarise themselves with each of the participating biodiversity infrastructures and network organisations, and also learn about the specific services they provide. There, anyone can explore various biodiversity data tools and services by browsing by their main data type, e.g. specimens, sequences, taxon names, literature.
While the project might be coming to an end, she pointed out, the BKH is here to stay as a navigation system in a universe of interconnected biodiversity research infrastructures.
To do this, not only will the partners continue to maintain it, but it will also remain open to any research infrastructure that wishes to feature its own tools and services compliant with the linked and FAIR data requirements set by the BiCIKL consortium.
Indisputably, the ‘hot’ topics at the EBR III were the novel technologies for remote and non-invasive, yet efficient biomonitoring; the utilisation of data and other input sourced by citizen scientists; as well as leveraging different types and sources of biodiversity data, in order to better inform decision-makers, but also future-proof the scientific knowledge we have collected and generated to date.
Project’s coordinator Dr Quentin Groom presents the B-Cubed’s approach towards standardised access to biodiversity data for the use of policy-making at the EBR III conference.
Amongst the other Horizon Europe projects presented at the EBR III conference was B-Cubed (Biodiversity Building Blocks for policy). On Monday, the project’s coordinator Dr Quentin Groom (Meise Botanic Garden) familiarised the conference participants with the project, which aims to standardise access to biodiversity data, in order to empower policymakers to proactively address the impacts of biodiversity change.
You can find more about B-Cubed and Pensoft’s role in it in this blog post.
Dr France Gerard (UK Centre for Ecology & Hydrology) talks about the challenges in using raw data – including those provided by drones – to derive habitat condition metrics.
MAMBO: another Horizon Europe project where Pensoft has been contributing with expertise in science communication, dissemination and exploitation, was also an active participant at the event. An acronym for Modern Approaches to the Monitoring of BiOdiversity, MAMBO had its own session on Tuesday morning, where Dr Vincent Kalkman (Naturalis Biodiversity Center), Dr France Gerard (UK Centre for Ecology & Hydrology) and Prof. Toke Høye (Aarhus University) each took to the stage to demonstrate how modern technology developed within the project is to improve biodiversity and habitat monitoring. Learn more about MAMBO and Pensoft’s involvement in this blog post.
MAMBO’s project coordinator Prof. Toke T. Høye talked about smarter technologies for biodiversity monitoring, including camera traps able to count insects at a particular site.
On the event’s website you can access the MAMBO’s slides presentations by Kalkman, GerardandHøye, as presented at the EBR III conference.
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The EBR III conference also saw a presentation – albeit remote – from Prof. Dr. Florian Leese (Dean at the University of Duisburg-Essen, Germany, and Editor-in-Chief at the Metabarcoding and Metagenomics journal), where he talked about the promise, but also the challenges for DNA-based methods to empower biodiversity monitoring.
Amongst the key tasks here, he pointed out, are the alignment of DNA-based methods with the Global Biodiversity Framework; central push and funding for standards and guidance; publication of data in portals that adhere to the best data practices and rules; and the mobilisation of existing resources such as the meteorological ones.
He also made a reference to the Forum Paper “Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms” by R. Henrik Nilsson et al., where the international team provided a brief rationale and an overview of guidelines targeting the principles and approaches of exposing DNA-derived occurrence data in the context of broader biodiversity data. In the study, published in the Metabarcoding and Metagenomics journal in 2022, they also introduced a living version of these guidelines, which continues to encourage feedback and interaction as new techniques and best practices emerge.
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You can find the programme on the conference website and see highlights on the conference hashtag: #EBR2024.
