In 2023 the Centre for Biodiversity Analysis hosted Rudolf Meier from the Center for Integrative Biodiversity Discovery at Berlin’s Museum fur Naturkunde for discussions on DiversityScanner. The novel technology developed by Meier's and Christian Pylatiuk's (Karlsruher Institut für Technologie) labs combines robotics, machine learning and high-throughput genomic sequencing to scan, classify and quantify invertebrate taxa from bulk environmental samples. 

We have continued to work with Meier, Pylatiuk and collaborators to bring this technology and associated workflows to Australia and initiated the establishment of the Australian Biodiversity Discovery Facility using the DiversityScanner technology. Our goal is to develop a facility where researchers and managers can bring samples for processing and training and to experiment and co-develop projects for the monitoring and discovery of Australia’s biodiversity.

The CBA now invites interested researchers, students, conservation managers and other stakeholders to an introductory open day to hear about and observe the DiversityScanner pipelines, and discuss potential projects to assist with testing and development of the technology for discovering, identifying and monitoring biodiversity.

Program

Download Open Day flyer

To help us plan for catering and lab tours please register by 18 November. If you can no longer attend in person, please let us know ASAP.

Expressions of interest for technology use trials

We are also seeking expressions of interest from people who would like to trial the use of DiversityScanner and associated pipelines for use in their research or monitoring projects. These trial projects will allow us to test the use and feasibility of the DiversityScanner technology across a broad range of Australian taxa and applications as we establish the Facility, and will provide you with a better understanding of whether and how this technology can work for your specific needs.

ANU Research Infrastructure Expo

The ABDF will also be at the 2024 ANU Research Infrastructure Expo on Wed 27 November.

References and further reading

Srivathsan, A., Lee, L., Katoh, K. et al. (2021). ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biol 19, 217. https://doi.org/10.1186/s12915-021-01141-x

Wührl, L., Pylatiuk, C., Giersch, M., Lapp, F., von Rintelen, T., Balke, M., Schmidt, S., Cerretti, P., & Meier, R. (2022). DiversityScanner: Robotic handling of small invertebrates with machine learning methods. Molecular Ecology Resources, 22, 1626–1638. https://doi.org/10.1111/1755-0998.13567

Rudolf Meier, Amrita Srivathsan, Sarah Siqueira Oliveira, Maria Isabel P.A. Balbi, Yuchen Ang, Darren Yeo, Dalton de Souza Amorim. (2023). "Dark taxonomy”: a new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment. bioRxiv 2023.08.31.555664; https://doi.org/10.1101/2023.08.31.555664

Meier, Rudolf, Hartop, Emily & Srivathsan, Amrita. (2024). Towards holistic insect monitoring: species discovery, description, identification and traits for all insects. Philosophical Transactions of the Royal Society B. 379. https://doi.org/10.1098/rstb.2023.0120

Artificial intelligence could help biologists classify the world's tiny creatures

DiversityScanner: AI-based Robotics Assist With the Discovery of Small Invertebrates

DiversityScanner: Robotic discovery of small invertebrates with machine learning methods

Accelerating Biodiversity Discovery in Hyperdiverse Arthropod Clades with Robots and Nanopore Sequencing