Course: Introduction to Image Analysis for Plant Phenotyping

Typically in plant phenotyping you might want to count or measure some feature of a plants physical shape. This video gives an overview of the ways in which image analysis …

What are the data types commonly used in Python, and how do we refer to them? We introduce and discuss integers, floats and strings and they are used in Python.

A quick look at a region-based segmentation using the Statistical Region Merging plugin in Fiji. The instructions are in the attached pdf in Downloads below. The image used in the …

Model-based region segmentation often involves some form of machine learning and training of the model using multiple images of similar subjects. This practical shows you how to try this out …

Hyperspectral images are usually captured in a slightly different way to standard RGB images. This video explains the push broom method, how it differs from RGB imaging, and the associated …

This week we expanded our discussion of image analysis to consider data types beyond 2D images. This includes: Video data, how it differs from still images and common video data …

Hyperspectral data is useful, but the sheer amount of data can be difficult to work with. This video explains how often the data is reduced to specific important wavelengths and …

This week we have tackled some of the core tasks in image analysis you will encounter time and time again. These include: Types of image noise and noise reduction The …

What are variables, and why are they useful?

The “Hello World!” program is a very simple program that just prints some text to the screen, and is often used as the introduction to any new programming language. Here’s …

An introduction to programming languages. In this course we will mainly use Python. In this section in particular we will use the script editor in Fiji.

How shape-based models are used in video or time sequence image data to track objects. We show how active contour models can be used not only to track objects, but …

This week we have looked at a lot of the important building blocks of programming and Python code in particular, while seeing how these tools can be used to code …

This week week in the course we have covered: Using Fiji to measure image features such as distance, angle, area, and how to calibrate those measurments Image histograms: what they …

What are the difference between video data and sequences of time lapse photographs? Usually video data has some sort of compression via a codec. In this video we discuss some …