Acquiring root images

Guillaume Lobet | 2012-06-16 | root image analysis

The image acquisition step is a critical one as it will determine the quantity of information contained in the final image. Fortunately, good images can be obtain fairly simply without buying fancy expensive material. In the next posts I will give simple tips to acquire nice root images with either a CCD camera or a scanner (which are probably the most widely used image acquisition devices as well as the less expensive). But first a small reminder on the image requirements. Image requirement In… More...

How to choose the right root image analysis tool

Guillaume Lobet | 2011-12-06 | root image analysis

In this post, I will try to point out the most important characteristics you will have to consider while choosing your root image analysis software. Very often, there is a strong link between an experimental design and the software used to treat the root images. Be careful that you should not be designing your experiment according to the available software in your lab, but the other way round. As there is more and more available software, the field of possible analysis widens. Do not hesitate… More...

What makes a root image suitable for analysis?

Guillaume Lobet | 2011-06-11 | root image analysis

The quality of an image is central if you want to get useful information out of it. Even the best software will not be able to analyse crappy images, so it is crucial to think about what makes a good image and how to acquire it. Usually, you will have the opportunity to improve your images at different steps of the process: the growth of the plant (substrate, ...) the image acquisition (the type of devise) the image preparation (thresholding,.. ) the image analysis (the type of measurement,… More...

Thresholding root images

Guillaume Lobet | 2010-12-15 | root image analysis thresholding

Many root image analysis procedures have a thresholding step in their workflow (e.i. WinRHIZO or EZ-RHIZO). The thresholding step aims at segmenting the original image (fig. 1A) in two parts: the "object" (the roots) and the "background", and to assign to each of them a different pixel value (typically 1 and 0). The subsequent binary image (fig. 1B) can be used, for instance, to generate a "root skeleton" (fig. 1C) or to estimate root diameter. Figure 1. A.… More...
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