Bioimaging Developer
Location:EMBL-EBI Hinxton near Cambridge, UK
Staff Category:Staff Member
Contract Duration:2 Years
Grading:5 (monthly salary starting at £2,552 after tax). For more information about pay and benefits click here
Closing Date:23rd March 2018
Reference Number:EBI_01157

Job Description

We are looking to recruit a Bioimaging Developer to join the Cellular Structure & 3D Bioimaging team at the European Bioinformatics Institute (EMBL-EBI) located at the Wellcome Genome Campus near Cambridge in the UK. EMBL-EBI is a world-leader in archiving and disseminating 3D biomacromolecular and cellular structure data. The Cellular Structure & 3D Bioimaging team plays a key role in the dissemination of 3DEM data through the EMDB ( and EMPIAR ( public archives. We develop and provide advanced tools and web-resources for searching, analyzing and visualizing structural data for the benefit of structural biologists and the wider scientific community. The team consists of an international and inter-disciplinary mix of professionals (scientists and IT specialists).

The remit of EMPIAR has recently grown from hosting raw 2D image data related to cryo electron microscopy experiments to 3D reconstructions from a range of cellular imaging modalities. EMPIAR could therefore scale very rapidly into the petabyte scale and in order to prepare for this eventuality we are undertaking a pilot project with the aim of developing a scalable storage solution for the public archiving of big imaging data (EMBL-EBI Bioimage Archive; BIA) and moving the EMPIAR back-end to exploit this solution. This is a joint project with multiple teams at EMBL-EBI including the Technical Services Cluster (led by Steven Newhouse) and the Functional Genomics Development Team (led by Ugis Sarkans). As a part of this project, the post holder will help develop the generic imaging ingest and consumption API’s for the BIA and will port EMPIAR systems (deposition/annotation/data-out) to use these interfaces to store/retrieve information to/from the BIA.

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 23 member states and two associate member states and proud to be an equal-opportunity employer. Our 600 staff are engineers, technicians, scientists and other professionals from all over the world.

Qualifications and Experience

Applicants should have a Masters/PhD degree in science, mathematics, computer science or a relevant discipline, and some experience in bioimaging or structural biology. Proficiency in programming (preferably Python) and developing software in a primarily Unix-based environment is essential.

Previous experience of dealing with bioimaging data programmatically would be desirable. Familiarity with development tools such as Git, relational (e.g., MySql) and non-relational databases (e.g., MongoDB), storage solutions for big data such as object stores, and data transfer technologies would be an advantage.

Excellent written and oral communication skills, fluency in English, ability to work in a team, and attention to detail are required. The position may require occasional travel.


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.

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.

Application Instructions

To apply please submit a covering letter and CV, with two referees, through our online system.

Additional Information

Applications are welcome from all nationalities - 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 project duration specified.

Applications will close at 23:00 GMT on the date listed above.