Does anyone know if there's a method/software out there that we can use
with ImageJ to quantify root colonization by fungal hyphae in confocal
microscope images? Our fungus appears green under the scope when we treat
it with wheat germ agglutinin + the fluorophore WGA-Alexa Fluor 488
(Invitrogen), which binds to chitin. Colonization is usually expressed as
percent of root length colonized. We will have roots of 400 plants, with
20-50 slices each, and would like to avoid painstakingly adding up the
colonization in the 2D slices ourselves.