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...

Twitter review of our pre-print

Guillaume Lobet | 2016-09-19 | open science preprint social media

Here is a twitter review of our latest pre-print: [View the story "Twitter reviewing + response" on Storify] More...

New pre-print: Using models to evaluate root image analysis pipelines

Guillaume Lobet | 2016-09-14 | image analysis modelling open science

Our latest pre-print is out ! For this research, we used a root model, ArchiSimple, to generate a large library of ground-truth root images (10.000). We then used this library to evaluate a root image analysis pipeline. We showed that, as it could be expected, the errors increased with the size and complexity of the root systems. The pre-print is available here: The data are available here: The codes are available here:… 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...
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