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 software engineering and systems administration in their application to neuroscience research, in particular volume electron microscopy-based connectomics.
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 UKRI’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.
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Academic qualifications and experience:
PhD in a relevant biological subject, or MSc / MPhil plus substantial experience in industry in the field of computer vision and machine learning.
Extensive research experience in analysing imagery of neurons, handling large collections of confocal microscopy stacks, registering multi-terabyte series of electron microscopy images, setting up cluster computing routines for automated data analysis, system administration skills in monitoring and managing petabyte-scale data storage servers and databases, and expertise in computer programming in python, javascript, SQL, and other programming languages.
In addition, the candidate will arrive with some experience developing novel algorithms and having published them in scientific journals or computer science conferences. Experience in using modern machine learning libraries such as PyTorch and their execution in GPUs, plus experience in several other programming languages, ideally Rust, Java, or C++, and Javascript, would be desirable. In particular, we seek a candidate with experience in developing new machine learning approaches to object boundary segmentation, in instance segmentation, and in quantitative methods for monitoring and improving the performance of software. Furthermore, the ideal candidate will be able to comfortably demonstrate and or learn, either Linux or *BSD operating systems, performing system administration tasks on servers, and executing software in GPU and CPU clusters for high-performance computing.
Technical skills and expertise:
Significant experience of and proven expertise in cutting edge research relevant to the project, and knowledge of the field.
The ideal candidate will have a background in bioimage informatics, with expertise in signal processing, processing algorithms in general and with specific expertise in instance segmentation, ideally in electron microscopy volumes, with ample experience writing custom software to handle image processing and image analysis tasks.
Particularly useful would-be comprehensive experience in and knowledge of:
• The development and application of cluster computing pipelines to process large sets of image volumes.
• CATMAID, Fiji, BiaPy and other open-source software platforms for handling neuroscience imagery.
• Knowledge of Drosophila larval neuroanatomy and the use of NBLAST to compare and identify neurons by morphology.
• Managing large datasets using system administrator skills in Linux and *BSD servers, and knowledge of databases such as PostgreSQL.
• The use of the Python programming language with evidence in the form of online version control repositories of software written by the applicant.
• The use of GPU and CPU computer clusters.
• Implementing algorithms into version-controlled software packages for use by others.
• Setting up datasets in FlyWire.
• Cloud computing with AWS or similar vendors.
• Programming languages including python, bash, R, Java, C++, SQL and Javascript.
• Work with version control systems.
Additionally, the candidate will have the ability to and evidence of:
• Write scientific manuscripts.
• Travel to and present at scientific conferences.
• Travel for work to visit other laboratories to work in collaboration.
Track record of research:
This will include discoveries and significant achievements, and published papers preferably first author.