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Research Software Engineer - Imaging

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The Rosalind Franklin Institute (the Franklin) is a new national Research Centre, funded by the UK government through UK Research and Innovation, dedicated to bringing about transformative changes in life science through interdisciplinary research and technology. As Research Software Engineer - Imaging you will be responsible for the delivery of the imaging strategy for the imaging software elements of the Franklin. Primarily this will be in the area of Optical and Electron Microscopy analysis, Electron Tomography processing and analysis, and image segmentation.

Electrifying Life Science is a major UK wide initiative funded by the Wellcome Trust spearheaded by the Franklin, Diamond Light Source and the MRC-LMB. The Franklin component of Electrifying Life Science has at its core, the AMPLUS project, an ambitious plan to revolution electron cryo tomography of biological specimens (cryoET). A partnership with ThermoFisher will see the delivery of two cutting edge electron microscopes (Dorothy and Hodgkin) that will sit alongside two state of the art plasma cryo FIBs (Rosalind and Franklin). The LMB-MRC team lead by Richard Henderson and Chris Russo, are working to deliver a low cost high performance electron microscope, cryoEM100. Diamond, led by David Stuart and Gwyndaf Evans (joint with Franklin) will deliver an entirely new high energy electron diffraction instrument to revolutionise crystallography.

As part of the Franklin efforts, lead by Jim Naismith and Mark Basham, we will recruit ten scientists, at different levels of experience to work alongside our existing team. We are looking for scientists with expertise in biology, hardware experts, cryo electron microscopists and software experts.

We are currently expanding and looking to recruit a Research Software Engineers (RSE) as part of its Artificial Intelligence theme, specifically to work on the Electrifying Life Science project.

We are currently looking for an experienced Research Software Engineer – Imaging with excellent skills in the following areas.

• Research Software engineering principles (revision control, testing, continuous integration, deployment)

• Practical experience with writing tomographic reconstruction, segmentation or model fitting software, especially with respect to Electron Tomography.

• Practical experience with post processing tomography or microscopy images to extract biological information.

• Numerical Python (Numpy, scipy, matplotlib)

We are looking to fill up to three roles at either staff or senior level therefore salary will depend on appointment level and experience of the appointed candidate.


The main responsibilities of these roles will include:

• Develop automated reconstruction methodologies within the Savu framework for Electron Tomography

• Develop automated segmentation approaches within the SuRVoS system for segmentation and processing of Microscopy and tomography data.

• Develop sub-tomogram averaging methodologies.

• Develop molecular fitting strategies for ET Electron denisty maps.

• Look to apply the methods developed as part of the Electron Microscopy work to other areas

• Accelerate the existing software with possible, possibly with the use of Accelerator cards such as GPGPU’s.

• Attend scientific seminars and meetings to keep up to date with developments in software and methodology.

• Disseminate results through writing papers and presenting at scientific meetings.

• Contribute to the public engagement in science programme of the Franklin.

Selection criteria


• A PhD (or close to completion) or equivalent in a relevant field.

• Practical experience of applying software engineering and computer science principles to scientific problems.

• Practical experience of writing software to work with volumetric scientific data.

• Practical experience of Python and its best practices

• Ability to co-ordinate multiple aspects of work in order to meet deadlines.

• Ability to work as part of a team as well as independently.

• Ability to solve problems using innovative and flexible thinking.

• Excellent organisational and communication skills.


• Experience of software development and deployment.

• Experience of working in an industry setting.

• Experience of Systems Administration for Linux, Windows or Mac.

• Practical experience of developing and applying tomographic algorithms.

• Practical experience of developing and applying semantic segmentation routines.

• Practical experience of developing and applying molecular fitting routines.

• Project management experience.

• Experience with accelerator card programming, such as GPGPU’s of FPGA’s.

• Experience of HPC Software development and application.

In return we offer:

• 25 days holidays

• Generous pension scheme (employer’s contribution currently up to 18%)

• Training and development opportunities for staff at all levels

• Bus pass discount scheme

• Access to employee discount platform

• Subsidised canteen

• Free on-site parking

• Campus location in beautiful countryside with social and sports clubs open to staff

Closing date: 13th November 2020, 9:00am

Applicants should refer to our Candidate Privacy Policy


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