View Vacancy -- Senior Investigator Scientist - Neurobiology - Dr Albert Cardona - LMB 1367

Open Date
09/09/2020, 14:20
Close Date
08/10/2020, 23:55
MRC Laboratory of Molecular Biology
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.
UK Research and Innovation is a new entity that brings together nine partners to create an independent organisation with a strong voice for research and innovation, more information can be found at www.ukri.org

MRC - 3
Cambridge
£39,216 to £52,470 per annum
Permanent
Science
Full Time
Overall purpose:

To lead on a range of projects within the group of Dr Albert Cardona at the MRC Laboratory of Molecular Biology (LMB), as part of an overall programme on cellular connectomics, developing and applying software tools for the mapping and analysis of synaptic wiring diagrams from volume electron microscopy and other imaging techniques.

Inspired ideas for research for the next 3-5 years in the context of the work of the division.

To play a major role in the work of the research group, through the conduct of research, introduction of new ideas, dissemination of research results, support and training of others.

Contribute to the strategic development of the group and of the division overall.

To be a focus of expertise on the usage and development of software tools for cellular connectomics, with particular emphasis on image registration and segmentation and the mapping of synaptic wiring diagrams, using methods from conventional as well as modern machine learning approaches to computer vision and pattern recognition as applied to volume electron microscopy of neural tissue.

Main duties:

•    Under the general leadership of the Group Leader, to be responsible for all aspects of the research projects, including defining the direction of the work, conducting the research, analysing the data, preparing the work for publication and disseminating the results at meetings.

•    To present your work at seminars within the laboratory and at external meetings.

•    To contribute to laboratory-wide discussions on developments within the laboratory, particularly in the use of new techniques or new equipment.

•    To contribute to the overall preparation of research for publication.

•    To disseminate research findings in the form of publications, presentations, and reports and thus support the QQR mission of the division.

•    To identify, develop and apply a broad range of techniques to pursue the research objectives.

•    To keep up to date with developments in the field, proposing or implementing changes of direction as necessary.

•    To train students, Postdoctoral Scientists and others, and line management of group members where appropriate.

•    To contribute to the MRC’s engagement with the public and in the translation of research findings into improvements in health care.

Key responsibilities:

The key responsibility is to undertake cutting edge research, aimed at key questions within the remit of the research group.  You will be expected to provide the intellectual energy and independent thinking necessary to deliver the research and to play a major role in shaping the overall aims and success of the group.

You will be expected to have the skill and understanding to be able to act independently in solving problems, many of which may require novel approaches.  This will require the integration of different activities to ensure the successful delivery of the research projects.

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

To interact effectively with a wide range of staff, students and others to ensure the smooth running of the research group.  This will include setting an example in the effective use of resources, training others in methods and use of equipment and taking responsibility for the use of communal facilities.

To take on responsibility for managing equipment.

To write scientific papers and to present at internal meetings and at conferences.
 
To ensure the research is conducted in accordance with good practice and in compliance with local policies and legal requirements.

To recognise opportunities for the creation of intellectual property and to cooperate in patent protection and in exploitation.

To secure appropriate external funding and hence staffing and resources for the project, to include preparing grant applications for external funding and developing protocols.

To manage existing collaborations, and establish new collaborations, both within the division and the LMB and with external establishments.

To have a broad, balanced and informed perspective of current scientific issues especially those pertaining directly to the area of cellular connectomics, volume electron microscopy, and nanometer-resolution neuroanatomy of neurons and whole brains.

To agree the overall strategic direction of your research.  You will be expected to take managerial and budgetary responsibility for your research projects, especially the procurement of external funding.

Line management responsibilities will be undertaken; these responsibilities, to include staff development and performance management, should be applied in accordance with the MRC’s policies and procedures.  Training will be given if necessary.

Working relationships:

You will report to Dr Albert Cardona and will liaise with other Research Support staff, Postdoctoral Scientists and students, not only in your group, but also across the LMB and with external collaborators.
Academic qualifications and experience:

PhD or multiple years of research experience in a relevant biological subject, namely neuroscience with a focus on neuroanatomy at the nanometer scale.

Extensive research experience in cellular connectomics, quantitative neuroanatomy, and the reconstruction and analysis of neuronal wiring diagrams from volume electron microscopy with manual and automatic methods.

Technical skills and expertise:

Essential:
•    Hands-on experience in the field of cellular connectomics: reconstruction of neuronal arbors from volume electron microscopy and synapse detection, both manually and automatically.

•    Experience in the generation of ground truth data for learning machine learning classifiers.

•    Graph-theoretic analysis of neural circuits.

•    Software engineering: adjusting software applications, compiling and running them in computing servers, CPU clusters and GPU clusters.

•    Experience in developing or applying machine learning frameworks for synapse detection and quantification in volume electron microscopy.

•    Proven experience in interacting with scientists from multiple disciplines and in particular with biologists.

•    Programming languages, especially python and the django framework.

•    Experience with GPU computing and its often performance-critical integration into other frameworks and workflows.

•    Experience with using machine learning libraries with python bindings such as keras or pytorch.

Desirable:
•    Application of machine learning approaches to image segmentation in 2D and 3D.

•    Familiar with microscopy file formats and high-performance image processing software libraries.

•    Knowledge of the Rust programming language and Javascript.

•    Triage of I/O bottlenecks and deployment of optimization approaches, continuously monitoring metrics to ensure consistently optimal computing performance.

•    Use of machine learning libraries with python bindings such as keras or pytorch, with the candidate having written code that uses these libraries and have contributed patches or documentation to these or related machine learning infrastructure projects.

•    Writing image file format parsers and writers.

•    Development of APIs for end-user consumption.

•    PostgreSQL database and knowledge of the SQL programming language.

Track record of research:

This will include discoveries and significant achievements, and published papers preferably first author.

Other relevant evidence of:

•    Independent working and decision making,
•    Excellent standards of research conduct,
•    Mentoring,
•    Originality,
•    Influencing skills,
•    Communication skills,
•    Leadership,
•    Intellectual Property.
The candidate will work embedded in an interdisciplinary group comprised of biologists, physicists, computer scientists and material science engineers, and is expected to service the software needs of this diverse group, aptly navigating the different cultures in communication and software engineering methods.  The candidate is expected to contribute to scientific publications, including contributions in the form of script-generated figure panels and other techniques related to the production of reproducible papers, where figure panels are generated by programs from the raw data, and to train lab members in these techniques.
The MRC is a great place to work and progress your career, be it in scientific research or the support functions.The MRC is a unique working environment where our researchers are rewarded by world class innovation and collaboration opportunities that the MRC name brings. The MRC is an excellent place to develop yourself further and a range of training & development opportunities will be available to you, including professional registration with the Science Council.

Choosing to come to work at the MRC (part of UKRI) means that you will have access to a whole host of benefits from a defined benefit pension scheme and excellent holiday entitlement to access to employee shopping/travel discounts and salary sacrifice cycle to work scheme, as well as the chance to put the MRC and UKRI on your CV in the future.

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