Tutorials & Resources

For getting started in image processing and data analysis, you can find here some basics, easy to follow tutorials. We wrote them primarily for being used in lectures and courses. However due to many request by the users of our facility, we decided to also share them here.

In addition, be sure to also check out our guides section.


ImageJ/Fiji is one of the most popular free, open source tool for image processing and data extraction at our facility. It is simple, powerful, extendable by plugins and supports scripting languages for an easy automation of image processing tasks.

Intro Fiji image processing (PDF, 2 MB)

Intro Fiji image processing demo data (ZIP, 64 MB)

Intro Fiji macro programming (PDF, 667 KB)

Intro Fiji macro programming demo data (ZIP, 12 MB)

Bitplane Imaris

Bitplane Imaris is a commercial software package for the visualization, segmentation and analysis of multidimensional microscopy datasets. Powerful 3D visualizations, a simple user interface together with wizard-based segmentation allows to achieve relevant results without extensive knowledge in image processing.

Intro Imaris image processing (PDF, 1 MB)

Ilastik Segmentation

Ilastik is a simple, user-friendly free open source tool for interactive image classification, segmentation and analysis. At the ZMB, we use it as a segmentation and particle tracking solution for projects where classical intensity based thresholding strategies fail. Ilastik learns from labels provided by the user through a convenient mouse interface. Based on these labels, Ilastik infers a problem specific segmentation.

Intro Ilastik image segmentation (PDF, 2 MB)

Intro Ilastik image segmentation demo data (ZIP, 2 MB)