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Fiji workshop February 2018

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. Also, Fiji is relatively modest with hardware requirements, as long as the files to work with do not get too big.

Anna Klemm from the Core Facility Bioimaging will give an introduction to this program in two four hour sessions. Participation is limited to 20.

To apply for this course please see below.

posterfiji2018-02-kleinDownload flyer.

Time and location

Wednesday & Thursday 07. + 08. February 2018,

in the computer 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.


The course fee is 50 Euros. Please register on this web page. Application deadline is on Friday, 19. January. Participation is limited to 20 so we likely will not be able to accomodate all applicants. Preference will be given to Core Facility Bioimaging users. But we will fill any slots which should be left with other applicants.

You can use a computer from the computer room or you can bring your own notebook which should have 2 GB of RAM or more.