Microscopy Imaging Center

Image Data Analysis

How it works

In collaboration with the Science IT Support (ScITS) unit, the MIC offers to the imaging community support for all questions related to image acquisition, processing, storage etc. You can get help for a wide range of requests, from a simple introduction to Fiji to custom software for image processing. The next section offers a non-exhaustive list of examples of the type of issues you can get help with. For larger projects including IT infrastructure, users might get additional help from the swiss research IT project EnhanceR via ScITS. You can address your requests to Guillaume Witz preferably via email. Please include in your request a short description of your problem and, if relevant, an example dataset (for large files, you can use e.g. the filesender service of SWITCH).

In addition to support, trainings in the field of image processing are offered within the MIC trainings. The ScITS unit also provides trainings in areas of more general nature (e.g. using the UBELIX cluster, programming in Python or R) that might be relevant for MIC members.

Examples of questions you might have

  • Where should I store my data?
  • What software should I use to visualize my 3D time-lapse data?
  • How can I customize Fiji using a script?
  • Does my CellProfiler pipeline make sense?
  • How can I get the necessary computing power to process my hundreds of Gb of data?
  • I need custom image processing for a new type of data. Can someone help?
  • I can’t open my data, connect to a server, run a Fiji plugin, etc. I need help!
  • Where can I learn to do some of the above things myself?

What the MIC-ScITS Imaging Support can provide

  • Discuss potential analysis strategies for your imaging project.
  • Find the right hardware combination for your needs and configure it (UBELIX, SWITCH, your local computer).
  • Define an analysis pipeline for your data, using for example Fiji, CellProfiler, Skimage, Ilastik etc.
  • Write custom scripts or software for specific applications.
  • Fix your day to day problems with software and infrastructure.
  • Organize a training.

Guillaume Witz, Imaging Specialist for MIC

Guillaume Witz has joined the Science IT Support unit of the University of Bern in September 2018 with the specific task of supporting MIC scientists. He obtained a M.Sc in physics and a Ph.D. in biophysics from EPFL, studying DNA biophysics with atomic force microscopy and numerical simulations. He then switched his research field to biology and spent several years studying the bacterial cell cycle using live cell light microscopy at Harvard University and the Biozentrum Basel. During that time he developed software solutions and pipelines to analyze large multi-dimensional data for segmentation, 3D reconstruction, tracking etc. using e.g. Fiji, Python, high-performance computing and machine learning.

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.