Facility data engineer

The University of Twente is setting up a unique facility for groundbreaking Organ-on-Chip research and development. Organs-on-chips are tissue cultures that are used to study human disease and aging. We aim to make these miniature organs as representative as possible, so that they can replace animal testing and advance personalized medicine.

The facility combines state-of-the-art bioprinting, tissue culture, microfluidics, sensors and microscopy. In addition to this high-end equipment, the facility will develop unique wavefront shaping microscopes for imaging inside the complex culture chambers that are used for growing the tissues.

One of the challenges in the facility is to handle large amounts of heterogeneous data, often coming from a variety of commercial and experimental systems. For a single sample, we may have device fabrication data, characterization data, time-lapse image stacks, segmented 3-D data, customized measurement scripts, etc. Often at different locations, on different devices, and by different users.

In order to streamline this workflow, we are looking for a facility data engineer. your primary task will be to set up an OMERO database for storing data and metadata, streamline the storage of terrabytes of imaging data, and interface the wide range of tools used by our researchers with this database. You will work closely with the researchers and facility staff and help in automating microscopy, writing scripts for connecting laboratory equipment, (cloud-based) image processing, and other aspects of the research.

• Enthusiastic about helping researchers with various scientific backgrounds in data and software engineering;
• HBO or master level education;
• Proven programming experience, ideally in collaborative open source projects;
• Proficient in Python and git;
• A basic understanding of data formats, servers, authentication, and databases;
• User oriented and hands-on: you are able to bridge the gap between information technology and users, providing concrete solutions that integrate in the imaging workflow.

You will collaborate with the data engineers of the NL-BioImaging AM consortium to learn the best practices developed at other Dutch imaging centers. In addition, you will be involved in training the users of the facility in data and software engineering.

We investigate the use of light for medical purposes. Our aim is to develop optical and hybrid optical-acoustical technologies for medical research and diagnosis, in particular in the fields of oncology, wound healing and microscopy. Physiological properties of primary interest to us are microcirculatory blood flow, hemoglobin concentrations, blood oxygenation and scattering properties in general.

Our approaches include physical research into light-tissue interaction and its measurement, biomedical engineering to realize suitable instrumentation for ex/in vivo use, and clinical evaluation together with several medical partners.