Microscopy Imaging Center

Data Science Lab (DSL)

The MIC collaborates closely with the Data Science Lab (DSL). The DSL offers trainings with high relevance for the analysis of bioimaging data and thus for microscopy. Further information and upcoming trainings can be found on the DSL website.

Some DSL trainings qualify PhD students of the Cutting Edge Microscopy (CEM) program to acquire ECTS through a topic-related presentation at a CEM presentation event. For more information on acquiring ECTS from attending a DSL course, please contact Ruth Lyck, the coordinator of the CEM PhD program.

Tools and Services

  • Image Processing with Python course
    Github repository with all the material for the Image Processing with Python course in the from of Jupyter notebooks.
  • Image processing station
    The MIC has acquired a powerful image processing station which is made available to the imaging community. The station, located at TKI, has 8 cores, 128GB of RAM and an NVIDIA Quadro P4000 graphics card, which makes it an ideal tool for processing and visualising large imaging datasets. The commercial software Imaris as well as standard open-source software such as Fiji are available on the station and additional software can be installed upon request. Any research group can ask for access to the computer either to test software, e.g. in planning the purchase of a station, or for projects requiring only occasionally high computing power. Access requests should be addressed directly to Guillaume Witz (guillaume.witz@math.unibe.ch) who will evaluate them and offer support to users.
  • Python Pandas course
    You want to learn how to efficiently handle multiple table outputs of Fiji or CellProfiler to make plots? This course will walk you through the Pandas package which is designed to handle tabular formats in Python. Basic and more advanced plotting examples are also given.
  • Fiji basics course
    Fiji (ImageJ) is the go-to tool if you quickly want to have a look at your imaging data and perform basic image processing. These are the slides used for the MIC course for Fiji beginners. If you follow them and try some of the exercises, you should have a good overview of basic Fiji usage.