Course: Introduction to Image Analysis for Plant Phenotyping

As described in the previous video, behind the scenes Python stores data in different ways depending on it’s type. You often don’t need to worry about this to begin with, …

Pixel-based segmentation is driven purely the image data itself, but model-based segmentation uses some prior knowledge about the object of interest, such as its shape, size or colour. This video …

Plant phenotyping commonly aims to identify objects in an image so they can be counted or measured in some way. Splitting an image into such regions or points of interest …

A first step is often to look at the intensity histogram of an image, to understand the data in the image. This video shows you how to do that in …

Noise effects single pixels, but some problems with images are global e.g. they are too bright, or too dark. This video discusses how to evaluate image contrast using image histograms, …

How can we reduce image noise? This video looks at some common techniques, including mean filtering and convolution.

The last important building block of computer programs that we’ll introduce in this activity are if statements. These are a way in which your program can make decisions based on …

Instead of running a loop a fixed number of times, as in a for loop, you might want to run it until some condition or other is met. To do …

What are libraries and how do we use them in Python? We’ve already seen one example of a library, ImageJ or ij. This video introduces another library, OpenCV, and shows …

A brief introduction to the IDE (Integrated Development Environment) Spyder, and how it differs from the script editor in Fiji.

Often when performing imaging analysis tasks, it’s not just one image that needs some post-processing but a whole series of images in a data set (e.g. a set of replicates …

Capturing good quality experimental images is vital if they are to be used for image analysis. This video notes some typical pitfalls encountered during image capture in changing environmental conditions. …

Often, the background and foreground in an image might be similar in brightness, but have distinct colours, or either the foreground or background might be a uniform distinct colour. In …

As discussed in the preceding video there are three main types of 3D representations of plants (or other objects), each of which has its own strengths and weaknesses. This article …

Image file formats There are a number of file formats we commonly encounter when working with digital images. Here we will look at a few properties of the most common …