BioImaging Bioinformatician

The revolution in imaging technologies has led to the need to share, integrate and reuse image data in a comprehensive way. EMBL-EBI’s imaging databases, EMPIAR and the BioImage Archive provide the means to store and search life science datasets from all imaging technologies at all scales and across all modalities.

These databases provide deposition and retrieval services to life scientists across the world. We are looking for an enthusiastic and motivated imaging bioinformatician who can work with researchers, imaging scientists, software developers and the wider BioImaging community to further develop these resources, with a focus on worldwide sharing of bioimaging data.

What you’ll do

You will be working to support our resources’ operational and data management development activities. You’ll support depositors to the BioImage Archive and EMPIAR, providing expertise, guidance and targeted curation. You’ll work with data generators, data consumers and networking organisations on data and metadata standards, both working with schema and tools directly and relaying needs and priorities to the core software development team. Using AI approaches to improve our operational activities will be a key part of the role.

As the BioImage Archive is a developing project, you will be able to shape its development, community and overall success. You’ll need to be keen to learn new approaches and technologies, work with a diverse global biological imaging community and engage with new imaging science.

The post provides a fantastic opportunity to work with a talented team to grow a key new resource at one of the world leading institutes for managing biological data.

Primary duties & responsibilities

• Support data deposition and import of data into the BioImage Archive and EMPIAR, providing expert advice to depositors, and developing data pipelines for complex submissions

• Work with the bioimaging community on standards, processes and tools for managing biological images, including programmatic implementation of metadata in schema languages, and participation in community format development, e.g. OME-Zarr

• Curate and standardise data and metadata across different scientific domains to address the needs of diverse bioimaging communities.

• Work with software developers within the BioImage Archive, EMPIAR and the wider EMBL-EBI teams to guide development priorities and test new features

• Create documentation and training materials to support users of the BioImage Archive

You will have

You should have a first degree in Biology, Bioinformatics, Computer Science or a related discipline, and a relevant higher degree such as a MSc. A PhD or equivalent work experience is preferred.

Skills and experience

• Good understanding of data collection, handling, visualisation, interpretation, archiving, dissemination etc. for at least one common imaging modality (e.g. light or electron microscopy)

• Experience developing scripts and tools for data transformation and processing (e.g. in Python, Julia or similar languages)

• Experience working with common data exchange formats, particularly JSON

• Demonstrated knowledge of research imaging techniques broadly

• Familiarity with data standards and ontologies, and experience with schema languages such as LinkML

Personal attributes

• Curiosity about science and bioimaging

• A strong desire to learn new skills and technologies

• Excellent communication and interpersonal skills

• Ability to work to tight deadlines

• The ability to work both independently and as part of a team

You may also have

• Post-doctoral experience in a life sciences research lab or bioimaging facility, either as a data producer or as a collaborator with data producers on microscopy data management and/or image processing

• Specific experience working with cross-modality biological data with an imaging component, e.g. spatial transcriptomics or spatial proteomics

• Specific experience working with emerging/next generation file formats, particularly OME-Zarr

• Experience with the management of research data, including understanding of and adherence to appropriate metadata standards

• Experience with bioimage analysis tools and techniques

• Experience working with semantic technologies including ontologies, data curation and JSON schema-based data validation

• Experience developing training materials and/or running training courses

Contract length: Grant-funded, 18 month fixed-term Staff Member contract.

Salary: Grade 5 - Monthly salary starting at £3,452.05 per month after tax but excluding pension and insurance contributions. Plus, generous benefits.

Next steps: This vacancy has a scheduled closing date of Wednesday, 2nd September and we welcome your application as soon as possible. Please submit and up- to-date CV and supporting cover letter outlining your transferable skills and experience and motivation for applying.

*** We will review applications on a rolling basis and so encourage candidates to apply as soon as possible. ***

Why join us
Do something meaningful
At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind's greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.

Join a culture of innovation
We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential. Watch this video to see how EMBL-EBI makes an impact.

Enjoy lots of benefits:

• Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances

• Flexible working arrangements - including hybrid working patterns

• Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)

• Generous time off: 30 days annual leave per year, in addition public holidays

• Relocation package including installation grant (if required)

• Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)

• Family benefits: On-site nursery, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances

• Benefits for non-UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance.

For detailed information please visit our employee benefits page here.

What else you need to know

• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Please take a look at our International Applicants page for further information.

• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.

• Diversity and inclusion: At EMBL, we believe that diverse teams drive innovation and scientific excellence. We encourage applications from candidates of all genders, identities, nationalities and/or any other diverse backgrounds.

• How to apply: To apply please submit a cover letter and a CV through our online system. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after the closing date.

Closing Date