Research Software Engineer – SMLM data assessment at King’s College London

Closing date: 20th September 2023

Full time post offered on a fixed-term contract until 31st August 2026

Salary range: Grade 6, £42,405 – £49,785 per annum, including London Weighting Allowance

Link to apply: https://www.kcl.ac.uk/jobs/074050-research-software-engineer

Informal enquiries to susan(dot)cox(at)kcl.ac.uk or sian(dot)culley(at)kcl.ac.uk

Job Description

Applications are invited for a Research Software Engineer to work on data assessment for single molecule localization microscopy in the Randall Centre for Cell and Molecular Biophysics within the Faculty of Life Sciences and Medicine at King’s College London. The position is funded by a 3-year grant from the BBSRC Bioinformatics and Biological Resources fund.

About the job

Single molecule localization microscopy (SMLM) is a popular super-resolution fluorescence microscopy technique which has become widely used over the last fifteen years. However, producing the final images in this technique is completely dependent on image analysis of large datasets (tens – hundreds of gigabytes), and this process is prone to generating artefacts which are not visually obvious and can lead to misleading results. Detecting these artefacts and determining image properties such as spatial resolution is crucial for ensuring that accurate biological conclusions are drawn from SMLM images. In this position, you will be working with the groups of Susan Cox and Siân Culley, two leaders in the field of SMLM data assessment, Nicholas Anthony from the KCL Microscopy Innovation Centre, and a postdoctoral colleague to develop new approaches to SMLM data assessment and integrate them into packages which are of wide use to the global microscopy community.

Roles and Responsibilities

Your work will focus on shipping the newly developed techniques in form usable by people who are not experts in programming: structuring the code base in a sustainable and maintainable way, improving memory usage and performance, transforming currently existing methods into usable packages and plugins (for example for ImageJ and napari), and user support for the packages you create. As new data assessment techniques are developed during the project, you will provide input and guidance into how to best implement these such that they are widely useful.

Key responsibilities

• Design approaches to convert methods to assess image quality into software which is useful to the microscopy community
• Optimise software for speed and memory performance
• Develop software into packages for both ImageJ and napari
• Support users of the software and resolve issues which users encounter
• Plan and troubleshoot own work
• Contribute to collaborative decision making with colleagues in area of research
• Work effectively to specific deliverables and to strict deadlines of this programme

Skills, knowledge, and experience

Requirements

• Science or engineering background with a degree in computer science, engineering, physics, chemistry or biological sciences or related discipline
• Proficiency in either Python, C++ or Java
• Experience in any of shell scripting, build systems, continuous integration/deployment, automated testing or any related area

Essential criteria

1. Undergraduate degree in relevant area (sciences, computer science or engineering)
2. Experience of software development in a research or commercial context
3. Fluency in at least one of: python, C++, java
4. Experience of software development to process images
5. Understanding of version control and its importance in software development
6. Demonstrated ability to plan and troubleshoot own work
7. Demonstrated ability to work effectively with others

Desirable criteria

1. PhD in relevant area (sciences, computer science or engineering, or about to receive a PhD in one of those areas
2. Experience developing ImageJ plugins or napari packages
3. Experience of handling and processing microscopy data
4. Experience of continuous integration

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