View Vacancy -- Imaging Data Engineer - Neurobiology - Dr Sven Truckenbrodt - LMB 2697

The MRC Laboratory of Molecular Biology (LMB) is one of the birthplaces of modern molecular biology and has played an important role in the development of many new techniques, most notably protein crystallography, cryo-electron microscopy, DNA sequencing and monoclonal antibodies. The LMB has a clear goal of understanding biological processes at the molecular level, with the ultimate aim of using this knowledge to tackle specific problems in human health and disease. We aim to tackle difficult, long-term problems, which often require investment over many years.

There are four scientific Divisions - Structural Studies, Protein and Nucleic Acid Chemistry, Cell Biology and Neurobiology. However, scientific collaboration between the different Divisions is extensive. Scientists are well supported by excellent scientific facilities and by the LMB Operations Group which maintains the core infrastructure and services of the institute.

The LMB provides an unsurpassed environment for both new and established researchers. Scientists are drawn to the LMB from all over the world, thus creating a lively and international community for the exchange of ideas and technical innovation.

Overall purpose: 

To work within the Molecular Brian Mapping research group of Dr Sven Truckenbrodt at the MRC Laboratory of Molecular Biology (LMB), within a programme aimed at developing computational tools to handle, parse, analyse, and represent optical microscopy imaging datasets. Specifically, to undertake tool development and research to investigate datasets that are:

1.    Large and volumetric, i.e. multiple tens to hundreds of terabytes composed of tens of thousands of individual images stitched together to cover hundreds of cubic micrometres in volume.
2.    Acquired via multiple rounds of imaging, i.e. requiring registration between imaging rounds.
3.    Multidimensional in nature, i.e. integrating dozens of information channels.

Main duties:

•    Develop, apply and deploy automated data handling pipelines designed to process large (tens to thousands of TB) optical imaging datasets.
•    Develop, apply and deploy data handling pipelines designed to process multimodal imaging data with dozens of imaging channels.
•    Source and adapt imaging data handling and processing tools from the community, and
•    Use the tools you develop and source to handle datasets produced in the group.
•    Develop documentation for the tools you build and make them deployable in a way that allows imaging scientists with little to no programming experience to use them, inside and outside of the group.
•    Work closely with experimental scientists producing multimodal imaging datasets, to understand the analysis needs and assist in data handling.
•    Work collaboratively and non-competitively with other scientists and engineers, both inside and outside the group.
•    Travel internationally to learn and teach at workshops or with collaborators, and to present data at scientific conferences.
•    Contribute to the LMB’s mission in the public engagement of science, and the translation of research findings into improvements in health care.
•    Assist in the training of PhD students and other members of the LMB.
•    To draft scientific papers, and contribute to the overall preparation of research for publication.

Key responsibilities:

Within the overall direction of the programme, the group, the remit of the project and in discussion with the Group Leader, you will make a significant input into determining the direction of the project within a three-year lifespan. 

To plan your own work and objectives on a 12-month basis and manage your experimental work within the project along with your supervisor.

To work with limited supervision to identify, develop, modify and apply the necessary techniques to achieve the goals of the project.

To introduce and apply new techniques across a wide range of disciplines and to have the creativity and initiative to develop novel approaches and methods where required.

To ensure the research is carried out in accordance with good practice and in compliance with local policies and legal requirements.

To contribute to the smooth running of the group, including the effective use of resources, training of others and taking responsibility for use of communal facilities.

To enhance your research and generic skills through a tailored development programme. 

Working relationships: 

You will report to Dr Sven Truckenbrodt and will interact and collaborate with other Postdoctoral Scientists, Research Support staff and students, not only in your group, but also across the LMB and with external groups as necessary.

Additional information:

This is a three-year training and development position for a Postdoctoral Scientist who has recently completed studies, is moving into a new research discipline or has limited experience of key transferable skills. We support Postdoctoral Scientists with a range of formal and on-the-job training, including:
•    MRC training courses.
•    External training and personal development courses.
•    One-to-one training with your supervisor and other Scientists.

You will commit to undertaking the following:
•    Developing and following a personal development plan.
•    Attending training courses.
•    Identifying additional training which will support you to develop your career.

Academic qualifications:

A Master’s degree in neuroscience, molecular biology, biotechnology or a related discipline, or due to complete in 6 months.

Technical skills and expertise:

Essential
•    Experience working with programming tools, e.g. Python. You have built and deployed your own projects using these tools.
•    Some experience processing and handling imaging data, including stitching of overlapping imaging frames and registration of offset data volumes.
•    Familiarity with data formats used in multidimensional array processing, such as Zarr.
•    Proficient in Linux and Windows operating environments.

Desirable
•    Experience with connectomics datasets, including morphological segmentations.
•    Experience with biological data analysis and able to communicate fluently with biologists about biological problems.
•    Experience with or excited about learning about information design principles for effective data presentation to show complex brain mapping data in a way that can be easily parsed by humans.
•    Experience with processing and handling large (tens to hundreds of TB) datasets.
•    Experience with high-performance and cluster computing.
•    Experience with RAID data storage systems.
•    Familiar with software tools used for microscopy image processing, such as ImageJ, FIJI, and MATLAB.

Track record of research:

You can present evidence of successfully executing research or tool development projects independently or evidence of contributing to the success of such projects. This evidence can be in the form of scientific manuscripts, references, public projects, data or tool repositories (e.g. GitHub), or any other relevant evidence.

Other relevant evidence of: 

•    You are drawn to research questions that cross traditional discipline boundaries, and you are comfortable with high-risk projects.
•    You are excited about working in an environment that imports tools for project management and communication practiced in start-up and industry environments into an academic setting.
•    You are motivated to learn new technologies and skills and recognise that this is a life-long process necessary for tackling tough research questions.
•    You are enthusiastic about tackling large projects collaboratively that would not be possible for individual scientists embedded into a traditional academic environment, because you believe that sharing credit for a highly impactful project can be both more rewarding scientifically and more impactful for your career.
•    You enjoy working with people who are different from yourself, and who bring diverse perspectives to the table that may challenge your own assumptions.

Additional information: 

The Molecular Brain Mapping research group:
•    We are a new lab that aims to connect three fields — brain mapping, molecular physiology, and behaviour. We believe that this integration of fields is necessary to understand how biological computation works, from processing environmental inputs to producing internal sensation and generating behavioural output.
    o       We use morphological segmentation to map the circuits involved in these processes.
    o       We use a variety of molecular readouts and tools to understand how these circuits work, all the way from cell identity to the nanoscale architecture of synapses.
    o    We use behavioural paradigms to develop and test hypotheses.
•    The central tool of our group is expansion microscopy — it allows us to bridge the worlds of brain mapping and molecular physiology. Expansion microscopy allows us to obtain multimodal information at nanoscale resolution: from cellular morphology (akin to EM reconstructions) to neuronal barcoding, protein multiplexing, and other modalities. The datasets we can generate using this technology are uniquely rich in information.

Applicants are required to submit a full CV and covering letter.

You must at all times carry out your responsibilities with due regard to the UKRI: 

•    Code of Conduct
•    Equality, Diversity and Inclusion policy
•    Health and Safety policy
•    Data Protection policy

Job descriptions should be reviewed on a regular basis and at the annual appraisal. Any changes should be made and agreed between you and your manager.

The above lists are not exhaustive, and you are required to undertake such duties as may reasonably be requested within the scope of the post. All employees are required to act professionally, co-operatively and flexibly in line with the requirements of the post, the MRC and UKRI. 

The role holder will be required to have the appropriate level of security screening/vetting required for the role. UKRI reserves the right to run or re-run security clearance as required during the course of employment.