Image Data Specialist - Euro-BioImaging

Employer
EMBL
Location
Heidelberg, Baden-Württemberg (DE)
Salary
EMBL Grade 5, depending on individual qualifications and experience
Posted
August 04 2021
Ref
HD02020
Position Type
Full Time
Organization Type
Academia

The Euro-BioImaging Bio-Hub hosted by the European Molecular Biology Laboratory (EMBL) is looking for a highly motivated image data specialist to technically support the Image Data Services of the European research infrastructure Euro-BioImaging ERIC (www.eurobioimaging.eu).

Euro-BioImaging is building and offering image data services to the research community. The Euro-BioImaging Nodes support their users in data management and quality control. This includes image acquisition for user projects, data management, quality control, primary analysis and transfer to home base as well as advice to fulfil the user's data management plan (according to FAIR principles: https://www.go-fair.org/fair-principles/). The Euro-BioImaging Bio-Hub at EMBL provides services for image data archiving as well as computational tools for image analysis and processing via the cloud. In the future, it plans to provide added-value data and knowledge bases for different domains of image data and extend the catalog of its cloud based services. The provision of such powerful image data services for the community is of importance not only for the users of the infrastructure but for the life science and computational science communities at large. In line with this mission, EMBL, as the host of Euro-BioImaging’s data services, has recently launched the BioImage Archive (https://www.ebi.ac.uk/bioimage-archive/) as a new image data resource for the global scientific community.

Your role

The successful candidate will be an integral part of the Euro-BioImaging Bio-Hub and the Image Data Services team at EMBL, Heidelberg, that is starting to provide technical and collaborative support for image data management and analysis requirements for and in close collaboration with Euro-BioImaging stakeholders (Euro-BioImaging users, Nodes’ staff, imaging communities, technology developers, industry, funders, related EU initiatives etc.).

Initially, the image data specialist will be involved in a European Open Science Cloud project, EOSC-Future, where modular, shareable, open, and FAIR workflows, integrated in Galaxy (https://usegalaxy.org/) will be developed, for submitting large image data sets to the BioImage Archive. The submission process will also entail conversion to the emerging community standard cloud compatible image data format, ome.zarr (https://github.com/ome/ngff).

The postholder will also be involved in further developing the ome.zarr format, for example, in terms of the inclusion of image analysis results. Participation in such collaborative projects will be an important part of the job repertoire. In the long run, the postholder’s technical expertise will guide the process of establishing community standards for image data and metadata management and image data analysis. This will be realised by establishing novel workflows and making them accessible, eventually facilitating the adoption of open science best practices by Euro-BioImaging stakeholders and the scientific community at large.

You have

We are seeking a team player with relevant technical expertise who is ready to learn and to take ownership and responsibility of the tasks.

The ideal candidate should have:

  • A university degree in either life sciences, computer sciences, physics or engineering, with multiple years of relevant professional experience, or a PhD.
  • Have experience in advanced light or electron microscopy techniques and image data handling.
  • Experience with software development in one or more programming languages like java, python etc.
  • Experience with or be eager to acquire image data management and analysis skills to provide optimal solutions for the different stakeholders.
  • Strong communication and organisational skills. A high standard of written and spoken English is mandatory.

This is a technical position where a high level of computational literacy is essential. The successful candidate is a motivated self-starter with a proven ability to work within a multidisciplinary team environment.

You might also have

  • Experience in submitting image data to public bioimage data repositories (IDR, EMPIAR, etc.)
  • Experience with workflow management systems such as Galaxy
  • Experience using bioimage data analysis software such as Fiji, Cellprofiler, etc.
  • Experience in actively contributing to the open source communities with bioimage data handling and/or bioimage analysis

Why join us

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation with a very collegial and family friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits.Excellent child care facilities are available on campus.

Options regarding work from home can be discussed.

What else you need to know

We are Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary laboratory with more than 1600 employees from many nations, operating across six sites, in Heidelberg (HQ), Barcelona, Hinxton near Cambridge, Hamburg,Grenoble and Rome. Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research.

The working language of the institute is English.

In your online application, you will be asked to include a cover letter, CV and the contact details of 3 referees.

Further information about the position can be obtained from Aastha Mathur (aastha.mathur@embl.de), Euro-BioImaging Coordinator Image Data Services; and Antje Keppler (keppler@embl.de), Director Bio-Hub.

Interviews are planned for September 2021. The initial contract is for a period of two years. Please apply online through: www.embl.org/jobs

Closing date: 31. August 2021
Contract duration: 2 years
Grading: 5, depending on individual qualifications and experience