A colour image processing algorithm is presented to identify and measure morphological features of mycelial aggregates in biomass stained with crystal violet to discriminate filamentous regions and compacted cores. The method improves the accuracy and allows automation of the previous monochrome procedure (Durant et al., 1994). It has been applied to the characterisation of aggregates from a shake-flask culture of Fomes fomentarius (Basidiomycete) presenting extended filamentous outer zones. The area of the whole pellet, core, and annular regions of each pellet were measured. The convex area ratio and annular fullness were estimated and means of each samples were calculated.