EMBL Heidelberg
Meyerhofstraße 1
Heidelberg, Germany

Image Processing & Analysis with ilastik

Code: Python
Last revised: 2019-07-29 15:30:55
Price: 30 EUR pro Platz (VAT excl.)
Location: Room 202, EMBL Heidelberg
Available seats: 20
Level: Beginners



Anna Kreshuk

Course Description

ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, automated and semi-automated segmentation of boundary-based objects, and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode.

Using ilastik requires no previous experience in image processing. This course is aimed at anyone who works with biological images and wants to learn to use ilastik to easily process and analyse their data. The course will be hosted by Bio-IT at EMBL.

Course Content

During the morning you will get an overview of ilastik and make your first steps in selected workflows.

In the afternoon you will have a chance to work on your own data, supported by the ilastik development team.  If you are already a proficient ilastik user, feel free to only join in the afternoon.


The course assumes no prior experience with ilastik. It will be hands-on: you should bring your own laptop with ilastik installed (see link below for installation instructions). For the afternoon session you can bring your own data to work on!



Registration is required, via the booking form in the official Bio-IT page. Members of other EMBL sites can choose to follow the morning session remotely through video conferencing. The external participants will be contacted after their registration by the course organisers with more detail about their participation.




Sponsored by the German Network for Bioinformatics Infrastructure (deNBI)