Root Image Analysis in ImageJ

View the Project on GitHub guillaumelobet/RIA

Simple root image analysis in ImageJ


Images need to be in black and white, with the roots in black, for a good analysis. If analysing shoot, please rotate the image such as the shoot is upside-down.


You’re done!

Using the plugin

Screencast of RIA-J



Cross-hori and Cross-vert For these, we scan the root system skeleton with a horizontal/vertical line. During the scan, at each y/x position, we count the number of roots crossing the line. We then compute either the maximal or mean number of roots crossed during the scanning. For the horizontal scanning, we divided the root system in 30 layers. So cross-hori-mean-# can be seen as a root number profile along the depth of the root system.

Coord / Diff / Cumul We dived the root system in ten equal layers. In each layer, we find the min and max x values of the root segments. With this, we can compute a shape of the root system, with only 10 pairs of x values.

Example of visual output


example output


example output


example output

Cite us

If you use RIA-J please use the following citation:

Lobet G, Koevoets IT, Noll M, Tocquin P, Meyer PE, Pagès L, et al. Using a structural root system model to evaluate and improve the accuracy of root image analysis pipelines. Front Plant Sci. Frontiers; 2017;8. doi:10.3389/fpls.2017.00447