Martin-Luther-Universität Halle-Wittenberg


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ImageJ/Fiji Workshop


  • Dr. Martin Schattet
    Institutsbereich Pflanzenphysiologie / Martin-Luther-Universität Halle-Wittenberg
  • Dr. Birgit Möller
    Institut für Informatik / Martin-Luther-Universität Halle-Wittenberg
  • Dr. Markus Glaß
    Institut für Molekulare Medizin, Core  Facility Imaging der Medizinischen Fakultät / Martin-Luther-Universität  Halle-Wittenberg


The ImageJ/Fiji workshop 2018 will be hosted by the Leibniz Institute of Plant Biochemistry (IPB) in Halle:

Leibniz Institute of Plant Biochemistry

Weinberg 3
06120 Halle (Saale)

On Thursday the workshop will take place in the seminar room of the IPB. You have to go to the MSV department, there to the end of the floor until stairs appear on the left. Take the stairs upstairs and you will get to the seminar room.

On Friday we will be in the Kurt-Mothes-Saal which is located directly left of the main entrance.

If you are not sure how to find the rooms you can ask at the reception desk of the IPB at the main entrance.


  • Thursday, 27th of September, 13:00 - 16:00
  • Friday, 28th of September, 09:00 - 12:30

On Friday after the official end of the workshop there will be time for your specific questions and problems. You can bring images from your research and we will be happy to give suggestions and advice on how to best analyze the images and extract the data you desire.


The course will cover a large variety of topics, e.g.:

  • basic facts about the nature of digital images
  • transforming raw data files to figures
  • placing scale bars and extracting histograms
  • basics of different file formats
  • segmenting and measuring objects
  • particle analysis
  • handling ImageJ plugins
  • basics of automating tasks


The course will be held in English.

What to bring?

The course will have hands on parts for which you need to bring your own laptop. It is also of advantage to bring a mouse since ImageJ/Fiji strongly relies on graphical interaction. Your laptop should have Fiji running and our sample files on its hard drive. The latest release of Fiji can be found on its webpage    If you encounter any problems during installation we will be happy to provide support, just write us an email.

How to obtain ImageJ and sample files?

We will use an up-to-date Fiji version during all course days. Please make sure that you have Fiji running on your laptop. You can download the latest version of Fiji from its webpage   

In addition, we will use different sample data sets. You can download the sample data from the cloud of the university.


Deadline for registration: to be announced

Please use the IPB registration page to register for both parts of the workshop:

Further Information about ImageJ

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