Is there a software available for averaging of the corneal topography, pachymetry or corneal epithelial thickness maps? It should preferably be capable of mapping of the standard deviations as well.
I believe open source software packages like QGIS and Grass GIS would perform the averaging and the topography analysis. The software packages are freely available online.
What I need is to layer/stack a large number of 2D-colour corneal topography maps in order to obtain a single map, showing average colours. The software that you recommend seems to be very elaborate and probably capable of such a task, but it seems to require general expertise in the field, beyond the capabilities of a clinical ophthalmologist.
Octave could be used for the job as well, if the maps can be exported in numeric form. Octave is just like Mathematica, but it is freeware. Only a few lines of code are required to read in data and calculate average values and standard deviations.