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: http://dx.doi.org/10.1101/074922 The data are available here: https://zenodo.org/record/61739 The codes are available here:… More...

plant-image-analysis get a (small) redesign

Guillaume Lobet | 2016-09-14 | image analysis database

After 3 years, the http://www.plant-image-analysis.org website got a small re-design. Nothing major, but small improvement to make the navigation easier. The main changes are on the front page, where we included the Isotope plugin for an easy sorting of the different tools categories. As a result, no more page re-loading is needed. We also change a bit the design of the front page, to include more information about every tool. Check it out! 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...

The current state of plant image analysis software tools

Guillaume Lobet | 2015-02-26 | image analysis

Nobody questions it anymore: image analysis is an essential tool in plant sciences. From the object detection algorithm used by the microscope software to the dedicated ImageJ plugin for rosette area measurements, images analysis tools and methods are presents in many plant researchers' pipeline. In this post, I will try to give a short overview of the existing plant image analysis tools (mainly with data coming from the plant-image-analysis.org website). I will also discuss some of the current… 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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