The Uhlmann research group develops mathematical tools for the analysis of bioimages. Our motivation is to provide continuous models to capture and characterize biological objects from image data, thereby bridging the gap between the digital nature of image processing algorithms and the analog nature of the natural biological world. Our work blends formal mathematics with computer science and image processing, and involves collaborations with researchers in various fields of biology.
This project focuses on challenging 3D Optical Projection Tomography (OPT) scans of developing mouse embryos at different life stages acquired by the Sharpe Group at EMBL Barcelona. Your role will be to develop an image analysis solution based on continuous deformable surface models to capture and characterise the shape of embryos and its increasingly complex features. It will include the formulation and implementation of the tailored 3D model per se, as well as the design of an automated procedure to fit it to the 3D image data and extract quantitative measurements characterising it. The final results will aim at providing a standard reference, a definitive reconstruction that both computational and experimental scientists would be able to use. Ultimately, such a 3D tissue geometry model could be linked with gene expression data. In a broader sense, the project thus opens the way to the development of a general theoretical framework for representing and characterizing 3D biological objects which deform over time, and making the link with local molecular information.
You have a PhD in computer science, mathematics or electrical engineering, with knowledge in differential geometry, solid python coding skills and experience with 3D image volume handling, rendering and processing, possibly using VTK. You have experience formulating and solving optimisation problems. You are interested in using your competences in the exciting context of bioimage analysis, involving large datasets and the necessity for precise image-based quantification.
You might also have
You might also have experience developing formal mathematical framework in the context of signal or image processing problems.
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 do I 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. 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.
The initial contract is for a period of two years.
|Location:||EMBL-EBI, Hinxton near Cambridge, UK|
|Staff Category:||Postdoctoral Fellow|
|Contract Duration:||2 years|
|Grading:||Year 1 stipend – £2,630.10 per month|
|Closing Date:||17 January 2019|
Applications will close at 23:00 GMT on the date listed above.