In order to extract important morphological parameters of neurons, two-dimensional image processing and three-dimensional reconstruction are pursued from z-series images acquired by confocal microscopy. Image processing allows us to realise filtering, segmentation of the object, and thus introduces simplifications for image analysis. In addition to a three-dimensional visualization, three-dimensional reconstruction allows computation of cells area. We used this way of computation to compare different populations of mice cerebellar Purkinje cells: wild type cells versus cells overexpressing NOGO-A protein, and wild type cells versus cells from NOGO knock out mice. The study reveals that there are differences in the morphology between the different groups: a decrease in volume and area in cells overexpressing NOGO-A, and an increase in volume and area in cells from knock out mice.