Course: Introduction to Image Analysis for Plant Phenotyping

Welcome back to Week 2 of the course. This week we look at using the Fiji tool, both to manually measure some features in some plant images, and also to …

It’s inevitible that sooner or later your Python code will fail and you’ll see an error message. This video covers some of the basics of how to read them and …

As we all know, video data contains a set of still images arranged in a sequence. This article shows you how to access frames at a specific time within a …

The final part of our overview on image segmentation methods. This video describes and demonstrates the spatial grouping method split and merge in more detail, using quadtrees.

A continuation of our overview of the main common types of image segmentation. In this video we look at clustering using the example of K-means clustering, and spatial grouping using …

Computers are particular good and repeating simple tasks many times, possibly with small changes each loop. One way to do this in Python and other programming languages is with a …

A look in more detail into the dilation algorithm code implemented in the preceding video. In the following practical exercise we will ask you to try and implement similar code, …

Images are a great way of capturing data from the world around us for later use. Image analysis seeks to formalise that process and quantify that data in some way, …

How to operate Fiji and use menu commands using Python in the script editor

We saw how to perform dilation on thesholded images in the previous videos. This practical gives you a chance to try this for yourself, as well as adapting the code …

It’s common to process and analyse images purely using Python, rather than through via Fiji. The OpenCV library is one way to do this. This practical shows you how to …

A continuation of our video demonstrating ways to make measuments using Fiji. In this section we look at measuring areas, angles, bounding boxes in images and show how to count …

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 …

An introduction to examining and manipulating image data using Python. We start with the familiar example of thresholding grayscale images, but using Python in the Fiji script editor. Don’t worry …

A common method of contrast enhancement is histogram equalisation. This video briefly explains the process, and highlights some positives and negatives of it’s use in image analysis.