The method of the 'densitometric physical fractionator' presented here realizes an accurate and reproducible stereological quantification, not requiring a motorized or controlled z-axis, of cell populations. It includes a special software for the calibration of the optics alignment of the microscope and a semi-automatic procedure that integrates specific densitometric functions for image analysis, to identify the reference volume and the particle profiles. This improves the identification of the cells significantly, reduces variability in the subjective choice of the particles by the operators, and allows a consistent saving of time during the analysis. The method is proved to be unbiased and the accuracy and reproducibility of the results has been validated through intra- and inter-operator analyses. Furthermore, it has been applied to calculate the loss of spinal motor neurons during pathology progression in transgenic mice for superoxide-dismutase Cu/Zn dependent (SOD1) mutants, a model of amyotrophic lateral sclerosis (ALS).