Course: Introduction to Image Analysis for Plant Phenotyping

In this video, we continue our look at noise reduction filtering techniques. We consider Gaussian filtering and Median filtering, and in which circumstances each should be used.

A quick look at how 3D plant model data can be analysed, including the use of skeletonisation and clustering. 3D models We’ve seen how 3D models of plants can be …

Image noise is a common problem in image analysis. But what causes noise, what are the different types of noise, and how can we recognise them?

In this article we introduce the Python and standard library, and the idea that Python can be extended using external packages. We mention several ways you can install packages on …

This article is designed for absolute beginners at using a command line. If you’re confident using a command line and navigating the directories of your computer, this section may be …

Python Before learning more programming or coding skills next week it’s worth taking some time to look at the different pieces of software you might use to run code on …

The previous video showed how to set thresholds manually and measure area in Fiji. But there are further automation steps you can take. Here, we introduce automated thresholding algorithms such …

Taking apart a digital image and putting it together again As we saw in ‘What is a digital image?’, digital images are just tables of numbers (or sets of three …

In this first video introducing Fiji, we show how it can be used to manually measure image features. The video also shows how to calibrate image measurements to real world …

The main topics we will cover during this six-week course are as follows: Week 1 – an introduction to image analysis: What is image analysis and how is it used …

The final part of our discussion of typical image analysis problems in plant phenotyping We look at examples of counting objects using machine learning, and using multiple images to reconstruct …

The use of machine learning methods in image analysis aims to overcome some of the difficulties found in object detection and classification. This videos introduces some of the main types …

This practical gives you the opportunity to look at some 3D plant canopy reconstructions, at various stages of development, similar to those described in the preceding videos. To view the …

What image formats are best suited for image analysis? While jpegs reduce image storage requirements some data is lost. Other formats such as tiff are lossless and so retain more …

We’re all familiar with digital images. But what data is actually contained within them, and how is it organised? We also discuss the difference between data in RGB (colour) and …