By Kevin Gruener, Doctoral Candidate, CNRS-IGFL.
When Anton Dohrn founded the first zoological marine station of the world in Naples, he wanted to offer a space for scientists from all around the world to conduct their research. His vision lives on 150 years later, when we, the ZooCELL doctoral fellows came to Naples to learn about elaborate microscopy techniques and AI-assisted image analysis.
The ZooCELL crew at the entrance of the Aquarium at SZN in Napoli.
The course started with an introduction to expansion microscopy by Karel Mocaer (COS, UHEI, Heidelberg), an easy to use and cost efficient technique that allows to increase the size of the sample and gain a better resolution without the need of better microscopes. Considering that most of our animals are smaller than a millimetre, this method allows us to get a better insight into our samples.
The following days focused on AI- assisted image segmentation organized by one of the fellows, Seth Frazer, and his colleague Benedikt Best (EMBL, Heidelberg). Image segmentation is an important step for all of our projects and this part of the course presented to us multiple ways and tools like WebKnossos and Ilastik, how we can tackle this important task.
While image segmentation is a central point in our network, this task is futile without a properly aligned dataset. Sanja Jasek (COS, UHEI, Heidelberg) presented two methods on how to handle, stitch and align our volumes: the FIJI plug-in TrakEM2 and the command line based approach FEABAS.
Properly annotating such large datasets, though, is not feasible alone. To address this issue, Sanja Jasek and Gaspar Jekely (COS, UHEI, Heidelberg) introduced the web browser based tool CATMAID, which they previously used to fully annotate the nervous system and connectome of the 3-day old larva of Platynereis dumerelii together with their collaborators. Additionally, RStudio can be used as a tool to illustrate all the annotations visually and cohesively.
Besides morphological data, we also want to collect transcriptomic information about our samples in 3D space. For this, Marco Grillo (Stockholm University, Stockholm) and Alvaro Crevenna (EMBL, Rome) introduced us to spatial transcriptomics by in situ hybridization. Within a few days, we covered sample preparation, image acquisition and computational Analysis.
Besides these exciting topics, we received interesting presentation on appropriate use of AI tools by Fabio Petroni (EMBL, Rome), sustainability in science by the sustainability team of EMBL and WebKnossos by Norman Rzepka (co-funder of Scalable Minds), and a workshop on science communication by Matthew Cobb and Amy Maxmen.
Outreach related activities during the practical.
Finally, we got an exclusive visit to the Biodiversity Gateway exhibit at Casina Pompeiana where we explored innovative tools and approaches for communicating science related to the Bay of Naples.. Also, we had the chance to exchange with the local non-profit organization “AssociazioneLife Onlus”, who works with young people at risk of marginalization and disadvantaged people. While we gave them an introduction to marine biology, they took us on a sailing trip in the bay of Naples with Mount Vesuvius constantly in the background.
Sailing excursion through the bay of Naples.