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Practical: Accessing pixel data by coding in Fiji

A practical tutorial on getting and setting pixel values in Fiji / ImageJ

A screenshot of Fiji with an image of a root system on a blue background open, next to the script editor with some code input

As well as using the menus to operate Fiji, you can also interact with it programmatically using the script editor.

This practical shows you how to both get and set pixel values using Python in the script editor in Fiji. It also shows you how Fiji/ImageJ deals with colour pixel values.

All the instructions are in the attached pdf in the Downloads section below.

The image used in the example shown above can be found here: roots.jpg

Please let us know how you get on in the comments below.

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This content is taken from The University of Nottingham online course

Introduction to Image Analysis for Plant Phenotyping

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Introduction to Image Analysis for Plant Phenotyping

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