Postdoctoral Fellow: Linking X-ray Imaging and Transcriptomics

About the team/job

A collaboration between EMBL Hamburg, EMBL Rome and EMBL Heidelberg has been awarded funding from CZI to link the detailed cellular morphology of a tissue with its repertoire of macromolecules: High Throughput X-ray Tomography to Target Transcriptomics (HiTT2T).

EMBL Hamburg has recently established HiTT (High Throughput Tomography) – an X-ray imaging workflow which offers a fast and high-throughput approach to 3D structural imaging and virtual histology characterisation of entire tissue samples within minutes. Separately, EMBL Rome have developed spatial-omics technologies that permit multiplex RNA detection in thin tissue sections. The ability to target the 2D-omics data production based on the 3D X-ray data has the potential to revolutionise our understanding of disease. With this proposal, we will move beyond the current state-of-the-art of the methodologies and go to high throughput volumetric tissue analysis and transcriptomics via the development of HiTT2T - High Throughput Tomography to Targeted Transcriptomics. Using the information obtained via HiTT2T and the power of computational analysis presents the possibility of predicting and/or preventing disease with a greater degree of accuracy in the future.

As part of this project there is an opportunity for a 3 year postdoctoral position at EMBL Hamburg to develop the X-ray imaging (HiTT) aspects of the project. The successful candidate will work closely with the EMBL Rome team to ensure sample preparation is optimised for both X-ray imaging and downstream post-imaging transcriptomics. In addition the successful candidate will work closely with the computational team at EMBL Heidelberg in order to ensure that maximum value is extracted from the 3D X-ray data and in particular with the position associated with vacancy notice HD02752.

Your role

This role in Liz Duke’s team at EMBL Hamburg will involve extensive use of a synchrotron facility, particularly the P14 beamine at PETRA III.

You will contribute to the development of high throughput X-ray tomography techniques applied to the imaging and analysis of tissue samples as part of the 3D X-ray to 3D transcriptomics workflow.

You have

For this role you have:

• A PhD in an area broadly relevant to tissue imaging in biology
• Computational experience in the handling and analysis of large volume 3D data sets
• An affinity for collaborative multidisciplinary work
• A good command of spoken and written English as the working language at EMBL is English

You might also have

You might also have specific expertise in one or more of the following areas:

• Detailed knowledge and understanding of biological X-ray imaging particularly in relation to its application to soft biological tissue.
• Experience with registration algorithms and targeting approaches
• Experience in 3D Image segmentation

Why join us

EMBL is curiosity-driven, community-oriented and international. As an inclusive, equal opportunity employer, we believe that diversity enables us to collaborate more effectively and be innovative in our approaches. We are, therefore, committed to creating an inclusive and flexible culture - one where everyone can realise their full potential and make a positive contribution to our organisation.

We encourage applications from individuals who can complement our existing team – we believe that success is built on having teams whose backgrounds and personal experiences reflect the diversity of the populations that our science serves. We actively encourage applications from all genders and cultures, ethnic groups and all demographics to help us avoid perpetuating biases and oversights at this transformational point in our people strategy.

EMBL offers attractive conditions and benefits appropriate to an international research organisation with a very collegial and family-friendly working environment. Competitive salary and social security benefits, financial support for relocation, a relaxed culture, professional development, and other staff facilities make EMBL a great place to work.

** Don’t meet every single requirement? We are dedicated to building a diverse, inclusive and authentic workplace, so if you’re excited about this role but your past experience doesn’t align perfectly with every qualification in the job description, we encourage you to apply nevertheless.

What else you need to know

We are Europe’s research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1900 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg, Grenoble and Rome.

Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. The working language of the institute is English.

EMBL is a signatory of DORA. Find out how we implement best practices in research assessment in our recruitment processes here.

Please apply online through: www.embl.org/jobs