LCAM-NKI ImageJ course (regular)


Title: ImageJ/Fiji course (Image processing & analysis)
9 & 15 June 2017
Contact: Marjolijn Mertz (
Previous editions:
spring 2017

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

This course runs multiple times a year.
The course is split over 2 days featuring theoretical presentations and interactive practice examples .



Module 1 Image Representation & ProcessingWhat is ImageJ/Fiji: Download, Installation, Basic Settings

First steps with ImageJ/Fiji : Menus, Online documentation, Image opening, Plugin installation

What is a numerical image: Detectors for microscopy, Image dynamic, Image formats

Basic Operations : Histogram manipulation, Images transformations, Making figures, Image calibrations, 3D visualization

Images treatment: Background subtraction, Filtering, Watershed

9:00-17:30(+30 mins Q&A)
Module 2 Image segmentation & MeasurementsImage analysis: Threshold, fluorescence intensity quantification, object counting, coloration analysis (threshold, color separation), co-localization, morphometric operations

Initiation to task automation: batch process, macro recorder, simple macro writing

9:00-17:30(+30 mins Q&A)


Target Audience: Employees NKI
2 days
Course organizers:
Digital Microscopy Facility, LCAM-NKI

More information:
Marjolijn Mertz
Digital Microscopy Facility
t: +31 (0)20 512 6080