DiversityScanner is novel technology developed by Rudolf Meier (Museum fur Naturkunde) and Lorenz Wührl and Christian Pylatiuk (Karlsruher Institut für Technologie) that combines robotics, machine learning and high-throughput genomic sequencing to scan, classify and quantify invertebrate taxa from bulk environmental samples. The Centre for Biodiversity Analysis has initiated the establishment of the Australian Biodiversity Discovery Facility to use and develop the DiversityScanner pipelines for Australian taxa.

Expressions of Interest for Technology Use Trials

The CBA is now 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 provide you with a better understanding of whether and how this technology can work for your specific needs.

We welcome EOIs (see Downloads) from anyone, including students, working in fields related to Biodiversity, who have samples available to be processed using DiversityScanner pipelines. We are looking for several test cases that represent a broad range of taxa and applications. If your EOI is successful we will work with you to determine the best way to process your samples. We will cover the costs of sample processing using DiversityScanner methods. This includes reagents, consumables, access to equipment, bench fees, and staff time. All funds will be administered by the CBA. We will not cover costs associated with collecting samples/specimens.

If you are interested in developing an EOI but are unsure what DiversityScanner is or whether it may be suitable for your application, please get in touch. On 26 November 2024 we are hosting an introductory Open Day at the Australian Biodiversity Discovery Facility at ANU where there will be the opportunity to hear about and observe the DiversityScanner pipelines and discuss potential projects.

Please note that this is an expression of interest to trial and develop the DiversityScanner technology. We cannot guarantee useable results. Data produced (images, sequences) will be openly available for use by all collaborators and the CBA expects co-authorship on any resulting publications.

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