Phil Benfey, of Duke University has two interesting protocols

In Situ Hybridization Protocol (for plant roots)

In Situ Hybridization is a method for showing the spatial and temporal expression of genes at cellular resolutions. Probes bind to RNA in the cell allowing the location of the RNA to be visualized.

Confocal Imaging of Roots

"Roots are relatively thin and have low background fluorescence, making them highly suitable for analysis with the laserscanning confocal microscope.Confocal microscopy is an excellent tool for imaging at cellular resolution...."

Check out Phil Benfey's website to view the protocols.