About the team/job
We are looking for an experienced post-doctoral fellow with a strong interest in biological image analysis to join the Birney research group at EMBL-EBI to work on a new ERC funded project in collaboration with the University of Heidelberg – IndiGene.
Over the last seven years dedicated work has lead to the establishment of the first near isogenic panel in vertebrates, the inbred medaka Kiyosu panel. The IndiGene project will make use of this new valuable resource to separate various sources of variation, primarily genetic variation, environmental variation and stochastic variation.
A major part of this work is the development of advanced image processing methods and feature extraction software to extract robust measurements from high resolution, complex imaging datasets. Assays will include, CT-scans of whole adult fish, high-resolution/high-throughput embryo imaging and complex free-swimming videos.
Reliable feature extraction from image datasets for detailed phenotyping across the Kiyosu panel is essential. There will be a need for detailed experimental protocols to be designed and agreed with laboratory staff to ensure the correct linking of imaging measurements. Developing well planned out experimental designs for phenotyping and image feature extraction will be an important part of the role.
The applicant needs to hold a PhD in Bioinformatics, Physics, Computer Science, or related fields and will have a track record in image processing applications. You should be skilled at developing software in a Unix-based environment as well as having an awareness of good computational practices and experimental design.
You might also have
Knowledge of current machine learning based methods applied to image classification problems would be highly beneficial. Experience in database design and implementation is not required but would be considered as an advantage.
The successful applicant will be part of a highly collaborative team working between groups at EMBL-EBI and the University of Heidelberg. There will be regular project meetings and interaction with both computational and laboratory staff so the ability to present results and discuss ideas using good interpersonal skills are therefore required. There will also be the opportunity to take part in a number of field trips to Kiyosu Japan to help design and setup phenotyping assays on wild medaka fish.
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.
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 do I need to know
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.
Applications will close at 23:00 GMT on the date listed above.