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Fiji workshop January 2017

Fiji is a popular software for image processing and image analysis in particular for microscopic image data. It allows most operations that microscopists need (see the software page for more details). The fact that it is freely available certainly helped to boost its popularity.

Anna Klemm from the Core Facility Bioimaging will give an introduction to this program in two four hour sessions. Participation is limited to 18 and everybody will have to bring a laptop computer. It does not need to be a partiularily fast one, Fiji is relatively modest with hardware requirements, as long as the files to work with do not get too big.

To apply for this course please see below.

Poster fiji-kleinDownload flyer.

Time and location

Tuesday & Thursday 17. + 19. January 2017,

in a seminar room at the BMC.


  • Basics of the basic: opening images and inspecting them. Updating Fiji and installing plug-ins. Online resources about Fiji. Tips and Tricks for faster handling.
  • Preparation of publication-quality images: insertion of scale-bars and time stamps, creating composite color images and montages. Do’s and don’ts of contrast enhancement.

  • Basic quantifications: Set measurements and measure structures of the image. Segmentation by setting a threshold value. Measure single objects by “Analyze Particles…” command. Creating a line profile.

  • Basic filters: Principle of filter kernels to smooth the image before segmentation. Removing background.

  • Plug-Ins: Introduction to useful plug-ins for tracking and counting of objects.


Participation is limited to 18. All have to bring their own computer which should have 2 GB of RAM or more. Preference will be given to Core Facility Bioimaging users. But if you are interested, please apply, even if the dead line already expired. The number of applications will have an impact on how soon this course will be repeated.

Application deadline is Friday, 16. December. The course fee is 50 Euros. For users of the Core Facility, this amount will be converted in a credit to be used for microscopy fees, provided the user actually joins the course. If the applicant does not show up at the course, the money is forfeit.

Please apply on this web page.