Post-doc data scientist microscopy at the UMCG Microscopy & Imaging Center

Universitair Medisch Centrum Groningen

Universitair Medisch Centrum Groningen

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Working environment

The Department of Biomedical Sciences and systems at the UMC Groningen focusses on post-transcriptional responses to cellular and metabolic stress centered around the themes cellular fitness and human health.

Automated, digitized electron microscopy (EM) has led to an enormous increase in data throughput. In the UMCG, large-scale EM (a.k.a. ‘Nanotomy’) is now routinely used and is at the forefront developing the pipeline of large-scale EM worldwide. The technique compares well to google-earth: relative large areas are recorded at nanometer resolution. Nanotomy acquisition is now routine in our research and is being implemented in (inter)national collaborative projects, leading an unprecedented rich database of implemented nanotomy in a variety of life science projects.
The Dutch roadmap for large-scale infrastructures (NEMI roadmap) will invest in a new 100x faster nanotomy microscope, to be placed within the UMCG microscopy and Imaging center (UMIC). The enormous amount of data (in theory 1 Pb/ week if the microscope runs 24/7) needs to be managed, and if possible, smartly reduced after acquisition.

We seek: A post-doc data scientist microscopy at the UMCG Microscopy & Imaging Center.

Job description

Within the Giepmans team of cell biologists/ microscopists we seek a data scientist coordinator to smartly analyze/ reduce and to manage this data, including application of the FAIR principles. You will bridge scientific research questions with large scale electron microscopy data with data management and analysis. Tasks include to professionalize the current nanotomy database, including automated search tools, password-dependent access etc. and make it ready for the next big data increase that is expected when the new investments arrives in 2020. Moreover, you will be exploit new AI protocols for smart computing on raw data. Direct data analysis needs to be pioneered (from raw images to scientific answers ) and thus with smart computing reduce the amount of (less relevant) data. You will collaborate with dedicated data managers for this project located at the Swertz lab (Big data in biomedicine), who are experts in innovative FAIR data management and three of his team members will be involved in the project making a catalogue for nanotomy data.

What do we need

The data scientist we are looking for:
  • Is highly motivated to continue a scientific career with a proven track record of published research
  • Has affinity in or prior skills with Omero, Python, Matlab iRODS, R
  • Flexible and demonstrated ability to function in a team, as well as in between teams (microscopy and data management indicated above) and hook up with European initiatives
  • Given the national infrastructure, support data from other microscopy teams nationally
  • A track record in organisation and communication of multi-centre scientific collaborations
  • Collaborates well in (inter)national consortia and with researchers from other disciplines
  • Communicates easily in speech and writing (English) for scientific public
  • Has affinity with IT for research, data stewardship and ethical legal aspects
  • Is independent, proactive, outreaching, binding

The UMCG has a preventive Hepatitis B policy. The UMCG can provide you with the vaccination, should it be required for your position.
In case of specific professions a ‘Certificate of Good Conduct’ is required.

What do we offer

Your salary will be a maximum of € 4.481 gross per month (scale 10), depending on your qualifications and relevant experience, based on a full-time appointment.
In addition, the UMCG will offer you 8% holiday pay, an 8.3% end-of-year bonus.
The conditions of employment comply with the Collective Labour Agreement for Medical Centres (CAO-UMC). English:
Employment basis: temporary for a period of 4 years (one year, with possible 3 years extension).

More information
For applications or more information see or contact Ben Giepmans, Team leader Department of Biosciences of Cells and systems, e-mail: (don't use for applying).

Applying for a job

Please use the the digital application form at the bottom of this page - only these will be processed.
You can apply until 1 September 2019.
Within half an hour after sending the digital application form you will receive an email- confirmation with further information.

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