The story behind the root image library

Graphical abstract of our paper Some days ago, our manuscript, Using a Structural Root System Model to Evaluate and Improve the Accuracy of Root Image Analysis Pipelines was published online in its final version. The road has been long to reach that point, but it was a very fruitful one. And it was, in my opinion, a perfect example of the utility of both preprints and peer-review. Let me explain. At the beginning, the paper was built around one simple idea: we can use structural plant models… More...

The story behind the Root System Markup Language

If you have ever analysed root system images, you might now the unspoken truth: it requires a great deal of time and efforts! Either you work with an automated tracing software (such as EZ-Rhizo or RootSystemAnalyzer) and as soon as the root systems are getting old (more than 10 days) you'll need to spend quite some time correcting the detection; or you work with a semi-automated tool (such as SmartRoot or RootNav) and you'll have to go through every single image to trace the roots. The good… More...

Rhizoponics, the story behind the paper

About two years ago, we (Laura Mathieu, Pierre Tocquin, Claire Périlleux and myself) started to think about an efficient way to monitor the development of the Arabidopsis root system from the seedling to the flowering stages. Why we needed something new... The first obvious solution was to try to grow plant in rhizotrons, which we did. Although the plants grew well and seemed quite happy, we weren't entirely satisfied with this setup for three mains reasons: we could not see all the roots, … More...

Using a camera to take vertical root pictures

Guillaume Lobet | 2012-06-19 | root image camera

One way to take root picture using a camera is just to hold your root system by the collar and take a picture. While this technique might be the fastest and the easiest one, it is also to easiest way to get a bad picture. Here is a couple of things to think of before taking such image. Use young plants Choose the proper camera and lens (A) Always place the camera at the same distance of the roots (B) Use a dark, matt background (C) Place a scale on the background (D) About the root system… More...

Using a scanner to take root pictures

Guillaume Lobet | 2012-06-18 | root image scanner

Using a scanner is the best way to have picture with a high contrast and resolution. However, the speed of the acquisition is rather slow compared to a camera, specially if the resolution is high. Spread your root carefully (A) Choose a sufficient resolution About the root system Scanning can be used with large root system as it is possible to separate the different root on scanner surface. It is important to carefully spread the root in order to avoid overlaps and crossing as much as… More...
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