Postdoctoral Scientist - Neurobiology - Dr Albert Cardona - LMB 1395

Updated: 26 days ago
Location: Cambridge, ENGLAND
Deadline: 05 Nov 2020

View Vacancy -- Postdoctoral Scientist - Neurobiology - Dr Albert Cardona - LMB 1395
Open Date
06/10/2020, 17:10
Close Date
05/11/2020, 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 - 4

Cambridge

£31,602 to £34,443 per annum

Fixed Term

Science

Full Time

3 years

Overall purpose:
To work within the group of Dr Albert Cardona at the MRC Laboratory of Molecular Biology (LMB), within a programme aimed at whole brain connectomics from volume electron microscopy.  Specifically, we are seeking to recruit a data scientist with at least a year of experience with densely labelled volume electron microscopy data of nervous tissue.  In particular, the candidate will be experienced in developing and applying machine learning frameworks for synapse detection and segmentation, neuron segmentation and proofreading, and quantification of neuronal structures in nanometre-resolution data sets imaged with volume electron microscopy, for the purpose of mapping neuronal wiring diagrams from volume electron microscopy.  The ideal candidate will have an academic track record in the form of authored publications in the arXiv, computer vision conferences, and scientific journals, as well as accessible source code repositories demonstrating past work.
The ideal candidate will have experience with the python programming language (at version 3+), and in the use of machine learning libraries with python bindings such as keras or pytorch, and has written code available in accessible source code repositories where it can be evaluated by third parties, and has deployed their code to both CPU and GPU clusters, and single servers with multiple GPUs.  The ideal candidate has applied all of the above towards the generation of over-segmentations of neuronal structures, and is familiar with approaches for post-processing (proofreading) to automatically agglomerate over-segmented neuron fragments into full arbors, using biologically grounded approaches such as microtobule or endoplasmatic reticulum segmentation for validation.
Main duties:
•    To undertake research aimed at whole brain connectomics from volume electron microscopy.
•    To identify, develop and apply a broad range of techniques to pursue the research objectives.
•    To present scientific work at seminars within the laboratory and at external meetings.
•    To contribute to laboratory-wide discussions on developments within the field.
•    To draft scientific papers, and contribute to the overall preparation of research for publication.
•    To contribute to the LMB’s mission in the public engagement of science, and the translation of research findings into improvements in health care.
•    To assist in the training of PhD Students and other members of the LMB.
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 3-year lifespan.
To plan your own work and objectives on a 12-month basis and manage your 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 Albert Cardona 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.
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 and the MRC.
Additional information:
This is a 3-year training and development position for a Postdoctoral Scientist who has recently completed their doctoral 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.
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 and the MRC.

Academic qualifications:
A PhD in one of the following: computer science, neuroscience, physics, math, engineering or due to complete it within 6 months.
Technical skills and expertise:

Essential:
Background in computer vision and machine learning, or a closely related field.  The ideal candidate will have a mixed background of neuroscience and mathematics, statistics, engineering or a related field strongly grounded in applied math in the other.
Experience in software engineering, particularly with python, and the crafting of programs and pipelines using libraries such as Django, keras, torch, scikit-learn, and related machine learning and computer vision libraries.
Experience in JavaScript for front-end UI development, and importantly with writing programs for GPU-based computing.
Experience with running programs in CPU and GPU clusters, debugging them, collating results.
Experience in connectomics, in particular neuronal arbor reconstruction using manual and semi-automated methods, proofreading, and automated synapse detection.
Familiar with connectomics concepts associated with neurite segmentation, agglomeration of over-segmentations, proofreading, and more.

Desirable:
Experience with electron microscopy imagery.
Experience in systems administration, backup, version control, and data management.
Experience in the graph-theoretic analysis of neural circuit wiring diagrams.
General neuroscience knowledge.
Track record of research:
This will include achievements and contributions to published papers.
Other relevant evidence of:
•    Commitment.
•    Originality.
•    Ability to communicate.
•    Working with others.


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.
Our success is dependent upon our ability to embrace diversity and draw on the skills, understanding and experience of all our people. We welcome applications from all sections of the community irrespective of gender, race, ethnic or national origin, religion or belief, sexual orientation, disability or age. As "Disability Confident" employers, we guarantee to interview all applicants with disabilities who meet the minimum criteria for the vacancy.
UKRI supports research in areas that include animal health, agriculture and food security, and bioscience for health which includes research on animals, genetic modification and stem cell research. Whilst you may not have direct involvement in this type of research, you should consider whether this conflicts with your personal values or beliefs.
We will conduct a full and comprehensive pre-employment check as an essential part of the recruitment process on all individuals that are offered a position with UKRI. This will include a security check and an extreme organisations affiliation check.

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