Image Processing PhD course 2021

Course details

In this course we will initially use Fiji to illustrate fundamental image analysis concepts, then expand to introduce other software packages such as cell profiler and Ilastik.

The students will learn what a digital image is, how and when to perform basic image processing tasks and how to combine such tasks to perform advanced image processing and segmentation, automated pixel classification and, 2D and 3D measurements. Furthermore, the student will learn basic Macro programming and how to automate analysis of many images.

The course will consist of a course preparation day (Friday August 28th - introduction to image formation, basics on Fiji and preparation of own projects) followed by 5 days of teaching (31st of August through 4th of September). The course program includes work on own project sessions with advice, supervision and support from the teachers (3 at least at all times). Within 1 week after the course, students will need to submit a course report based on the outcome from their own project.

You can read more about the course and the take a look at the course description in the PhD school course catalogue. 

Teaching faculty

  • Sebastien Tossi
  • Chong Zhang

Assisted by

  • Thomas Braunstein
  • Clara Prats
  • Pablo Hernandez Varas

Registration for the course

If you are a PhD student you can register for the course through the PhD school for free (a direct link will be available soon).
If you want to participate in the course, and you are not a PhD student, you can use this form to register. The cost will then be 2500DKK.

Max number of participants: 18


All participants are expected to bring their own laptop, which should meet the following requirements:
1)      A minimum of 2 GB main RAM
2)      A graphic board compatible with Fiji 3D viewer*
3)      At least 10 GB available on the system partition
4)      The ability to connect to internet through WIFI
5)      A USB 2 or USB 3 port.
* To test if your graphic board is compatible with Fiji 3D viewer: call File > Open samples > Fly brain and Plugins > 3D viewer. Use the default settings of the 3D viewer and press "OK". You should see the 3D rendering of the image stack and also be able to interact with the volume with the mouse.

Students will have to submit an image processing project before the course; summarizing a bioimaging experiment and describing the research question.