About the team/job
We are looking to appoint a highly motivated scientist to work in the area of high-throughput imaging and image data analysis. The position will be based in the laboratory of John Marioni at the EMBL-EBI and will work closely with the team of Omer Bayraktar at the Wellcome Sanger Institute. The role will primarily support the computational aspects of tissue imaging. The methods developed will be applied to data generated as part of the international Human Cell Atlas project.
To date, single cell genomics, specifically single-cell RNA-sequencing, has revolutionised our ability to understand cell type heterogeneity in contexts ranging from the mouse embryo to terminally differentiated human cell types. However, most existing protocols require cells to be dissociated, meaning that the spatial location of a cell within its tissue of origin is lost and, consequently hindering a deep understanding of tissue organisation and cell type heterogeneity.
Recent technological advances have overcome this problem, meaning that a cell’s transcriptome can be assayed within a spatial context via tissue imaging. However, computational methods for analysing such data are in their infancy with, for example, substantial challenges remaining in image segmentation and cell identification.
The primary objective of this role is to support high-throughput imaging and image data analysis in the laboratory of John Marioni at the EMBL-EBI, working closely with the team of Omer Bayraktar at the Wellcome Sanger Institute. The role will primarily support the computational aspects of tissue imaging. The methods developed will be applied to data generated as part of the international Human Cell Atlas project. The candidate will be responsible for developing computational pipelines for high-throughput microscopy, image data analysis and metadata management. An ideal candidate is also expected to contribute to the development of bespoke microscopy pipelines, although experience with imaging instrumentation is not essential.
You will have a bachelor’s degree in biology, physics, computational science or a related area. A PhD in one of these subjects is desirable.
You must be able to demonstrate previous research and/or work experience in a computational image analysis group, microscopy core or company. A background in high-throughput microscopy, image data analysis and image metadata management is essential, as is prior experience with open source microscopy-control and image analysis pipelines.
You must have excellent communication skills and an ability to work well within a team.
You might also have
Previous experience with image databases and rendering solutions is desirable, as well as experience in building and maintaining bespoke microscopy instrumentation.
Why join us
At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 22 member states and two associate member states. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 600 staff are engineers, technicians, scientists and other professionals from all over the world.
EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. For more information about pay and benefits click here.
We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.
If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.
What else you need to know
To view a copy of the full job description please click here
To apply please submit a covering letter and CV through our online system.
Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. Visa information will be discussed in more depth with applicants selected for interview.
EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone.
This position is limited to the grant duration specified.
Applications will close at 23:00 GMT on the date listed above.