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...

Story behind the papers

Guillaume Lobet | 2015-01-27 | open science literature

Published papers are only the tip of the research iceberg. The visible part is often a fraction of the results acquired over the years while the hidden part is made of sweat and perseverance. Of repeated cycles of failures and success. Of (lonely) hours in the lab or in front of a computer. Of writing, submitting, re-writing, re-submitting. The hidden part is where the people (we, as scientists) are. So, often, when I read a paper I wonder about the story behind the project. When did it start… More...

Plant Image Analysis Papers

Guillaume Lobet | 2012-08-12 | image analysis literature

Not all papers on root image analysis present a new software and therefore I do not present them on this website. However, some of them are worth reading since they can bring new perspectives or methods that can be useful for all root researchers. So in order to be able to share all the interesting papers I read on root image analysis, I decide to create a group on the Mendeley website (Mendeley is a free citation manager with several sharing and social features). I am therefore delighted to… More...
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