Technical Officer: X-ray Imaging of Marine / Plankton Samples acquired during the TREC Expedition in Hamburg bei European Molecular Biology Laboratory

EMBL is Europe’s research laboratory for the life sciences – an intergovernmental organisation with more than 110 independent research groups and service teams carrying out research across the life sciences. We operate across six sites in Heidelberg (headquarters), Barcelona, Grenoble, Hamburg, Hinxton (near Cambridge) and Rome.

Our mission is to perform basic research in the life sciences, train scientists, students and visitors at all levels; offer vital services to scientists in the public and private sectors within the member states; develop new instruments and methods; and engage actively in technology transfer.

TREC (Traversing European Coastlines) is a flagship project of Planetary Biology, one of the transversal themes launched by EMBL’s new Programme “Molecules to Ecosystems” 2022-2026. With TREC (https://www.embl.org/about/info/trec/) , a journey through European coastlines is taking place in order to explore the biodiversity and molecular adaptability of microbial communities as well as key selected organisms. There is a focus on coastal habitats as they are the richest in species biodiversity and they also often present the highest levels of pollution. By combining the expertise and infrastructure of EMBL alongside other European partners, TREC aims to initiate a new era of coastal ecosystems exploration with the goal to observe, model and understand the effects of changing environments on organisms and communities, at the cellular and molecular levels.

As part of the TREC Expedition, marine samples are collected and processed by the EMBL mobile labs (https://www.embl.org/about/info/trec/mobile-labs/) at various locations along the European coastline. Some of these will be prepared in resin blocks for cellular electron microscopy. The aim is that these blocks are then imaged using X-rays and the HiTT technique (https://www.embl.org/groups/duke/) in order that their contents are catalogued and documented thus informing and directing further downstream imaging.

The key focus of this position is the collection and curation of the X-ray data on the TREC sample blocks. You will work within the Duke Team at EMBL Hamburg and in close collaboration with TREC scientists both in the field and at EMBL Heidelberg to deliver high quality X-ray data to support and develop this ambitious project.

In addition to the establishing the streamlined collection of HiTT data on the TREC samples there will be the opportunity to develop, optimize and establish methods to quantify and document the samples in order that the end users potentially interested in their contents can make informed decisions (e.g. based on taxonomy) about the next steps for each of the blocks. This will include handling, automation and visualisation of large volumetric imaging data sets. Additionally, for those interested there is the possibility to have a closer involvement with the block preparation process. Vital to the success of the project is the collaborative spirit between all parties involved in the project in order that the scientific outcomes of this ambitious project will have long lasting and far reaching consequences particularly on our understanding of the how the environment impacts on our coastal ecosystems.

Contract duration: 3 years

Grading: 6 or 7; depending on experience and qualifications (monthly salary starting from 4.3k EUR after tax + other paid benefits)

Reference number: HH00223

• A PhD or equivalent relevant experience in an area relevant to X-ray imaging
• Experience of image processing and/or 3D image segmentation
• An interest in the application of X-ray imaging to the study of large volumes of marine based samples
• An affinity for collaborative multidisciplinary work
• A good command of spoken and written English as the working language at EMBL is English

• Detailed knowledge and understanding of biological X-ray imaging
• Experience in sample preparation for x-ray imaging and/or (volume) electron microscopy
• Computer programming and software development for data analysis (preferably Python and/or C++)
• Experience in the handling and structuring of large three dimensional data sets
• Experience in database creation and image and information curation
• Experience using UNIX/Linux command line interfaces and/or cluster based computing resources

EMBL is curiosity-driven, community-oriented and international. As an inclusive, eq