Basic ImageJ/Fiji course

– image 
processing and analysis –

ImageJ or FIJI (stands for Fiji Is Just ImageJ) is a public domain image processing and analysis program. It is freely available

The main objective of this course is to give the microscopy user a global understanding of the huge potential of the program. We will go through all functionalities of the basic package and present specific tools for use in (cell) biology. During the course we will also review concepts and principles of image processing in general, in order to set a theoretical background.

The course is split over 3 days, both featuring theoretical presentations and interactive practice examples, and is intended for all who are interested in image processing and analysis.

This course will introduce the basic concepts of microscopy image analysis, such as color handling, bit depth & multi-channel images. It will cover image processing in ImageJ and an overview of the many ​ image analysis functions within this free software package. We will show you how to open images from proprietary file types (such as Leica .lif and Zeiss .czi files), how to get from raw data to a multi-panel, multi-color paper or talk figure, create multi-color images, add scale bars, work with hyperstacks, and install and use plugins and macros. You will learn how to enhance and filter images, use multichannel images and stacks, and perform basic analysis such as counting cells, segmentation and intensity analysis. In the afternoon session of day 2, we will cover more advanced analysis, identification of cell subtypes in multichannel images, colocalisation and how to record macros. In day 3 (not a full day) we dive a bit deeper into macro writing, cell tracking, and learn how to use a few cutting-edge tools in image processing and analysis.



Target audience:
Registration deadline:

March 21 & 28 + April 4, 2023. NOTE: You have to commit to days 1 and 2, from 9:30-17:30. These modules cannot be attended separately. Day 3 (10:00–16:00) is optional.
NKI-AvL and VU campus

For all who are interested in image processing and analysis
Free of charge
Marjolijn Mertz, Bram van den Broek, Amelie Dick, Rolf Harkes 
February 20, 2023