Martin-Luther-Universität Halle-Wittenberg


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ImageJ Course


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


Attention, the location of the course has changed!

The new location where the course will take place is:

Institute of Computer Science
Von-Seckendorff-Platz 1  
06120 Halle / Saale

Conference Room 5.09  (5th floor/attic floor)

Map showing the location of the Institute of Computer Science at the Von-Seckendorff-Platz - search for the blue arrow on the map
umgebungskarte-marker-license.pdf (11,1 MB)  vom 12.09.2017


  • Wednesday, 4th of October, 13:00 - 17:00
  • Thursday 5th of October, 13:00 - 17:00


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 language of the course will be chosen according to the audience, i.e., the courses will either be held in German or English depending on the language preferences of the participants.

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. These will be available from here due in time.


Deadline for registration: August, 31st, 2017

Please send an email to .

Please note: the number of participants is restricted to 30. Registrations will be sorted by the arrival time of the email, respectively. If there are more than 30 registrations for a day, a waitlist will be opened.

Further Information about ImageJ

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