Skip main navigation

Practical: Colour segmentation and thresholding

A practical on colour and grayscale thresholding using Fiji / ImageJ
Colour thresholding in Fiji. The left panel is the original image of red seeds on a blue background. The middle panel has histograms of Hue, Saturation and Value, and the right panel has the segmented image of black seeds on a whote background.
This practical gives you an opportunity to try out image thresholding on both colour and grayscale images, as described in the preceding videos.

All the instructions are in the attached pdf (see Downloads below). If you haven’t already, you will need to download and install the free software package Fiji from

The two image files we use in the practical are:

(Right-click on the image, then Save as…)

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

This article is from the free online

Introduction to Image Analysis for Plant Phenotyping

Created by
FutureLearn - Learning For Life

Reach your personal and professional goals

Unlock access to hundreds of expert online courses and degrees from top universities and educators to gain accredited qualifications and professional CV-building certificates.

Join over 18 million learners to launch, switch or build upon your career, all at your own pace, across a wide range of topic areas.

Start Learning now