For the Bioimage Core facility, everything revolves around the microscopes. It is our primary concern to make this technology accessible to the facility users. The microscopes use the biggest part of our budget, occupy most of our workspace and make up for the biggest chuck of our workload. However the facility users should keep in mind, that the data acquisition is the first part of the work to gather new insight.
The acquired data will need stewardship and more often than not, it needs to be processed and analysed by more than just the naked eye. Therefore our core facility also provides infrastructure for data management and bioimage analysis tailored to microscopy data.

  • Data acquisition

    This service can be broken down into the following activities:

    • Acquisition of new microscopes:
      Evaluating use cases, organising demonstrations
    • Instrument maintenance:
      Trouble shooting, quality control, small maintenance, coordinating service engineers
    • User training on the microscopes
    • Consulting for experimental setup
    • Assistance to optimise data acquisition (sampling, time, etc.)
  • Data management

    Central IT services of the university cover many general needs of scientists with their file storage infrastructure and their scientific-IT division. Additionally, the Research Promotion office assists scientists to elaborate their research data management plan, which is required for grant applications by most funding organs nowadays. Our core facility aims to complement these services with IT solutions specifically tailored to the microscopy data.

    Data produced with microscopes presents users with the challenge of handling a multitude of file formats encoding the pixel and metadata. Futhermore the visualisation of these data presents a challenge of its own. 

  • Data analysis

    With the introduction of sCMOS cameras and an increasing degree of automation on the microscopes, the data volumes produced with light microscopes grew significantly from megabytes to tens and hundreds of gigabytes. These complex datasets need on one hand software that caters to their specific needs for analysis and on the other hand computing infrastructure capable of handling these big data volumes.

    Our core facility provides its users with specialised software for visualisation and processing of multi-dimensional datasets. Furthermore some dedicated image analysis workstations are part of the facility infrastructure.