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...

Some news from plant-image-analysis.org

Guillaume Lobet | 2016-12-22 | plant image analysis json api image dataset

In the last few weeks, I made some changes and additions to the plant-image-analysis.org website, and I thought it might be time to present all of them. Redesign First, the front page changed a little bit, with an easier navigation / selection of the different tools. Instead a requiring a re-loading of the page for every selection, the filtering is now done dynamically using Isotope. It is faster and more fluid than it used to be, without impacting the initial page load. Datasets Then, I… More...

Creating graph with PubMed data

Guillaume Lobet | 2016-11-04 | bibliometrics r pubmed

A couple of days ago, I was looking for a way to create a citation graph from list of DOIs using R. It turned out that, although packages exists to get basic citation information from Google Scholar (with scholar), Scopus (rscopus) or CrossRef (rcrossref), informations about citing article is pretty much closed. The only site that allowed it was PubMed, with the drawback that it only analyse its own database. Here is how I did it. First, we start with a list PubMed ids, for which we would… 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: http://dx.doi.org/10.1101/074922 The data are available here: https://zenodo.org/record/61739 The codes are available here:… More...
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