This paper presents a system for computer-assisted quantification of axo-somatic boutons at motoneuron cell-surface membranes. Different immunohistochemical stains can be used to prepare tissue of the spinal cord. Based on micrographs displaying single neurons, a finite element balloon model has been applied to determine the exact location of the cell membrane. A synaptic profile is extracted next to the cell membrane and normalized with reference to the intracellular brightness. Furthermore, a manually selected reference cell is used to normalize settings of the microscope as well as variations in histochemical processing for each stain. Thereafter, staining, homogeneity, and allocation of boutons are determined automatically from the synaptic profiles. The system is evaluated by applying the coefficient of variation (Cv) to repeated measurements of a quantity. Based on 1856 motoneuronal images acquired from four animals with three stains, 93% of the images are analyzed correctly. The others were rejected, based on process protocols. Using only rabbit anti-synaptophysin as primary antibody, the correctness increases above 96%. Cv values are below 3%, 5%, and 6% for all measures with respect to stochastic optimization, cell positioning, and a large range of microscope settings, respectively. A sample size of about 100 is required to validate a significant reduction of staining in motoneurons below a hemi-section (Wilcoxon rank-sum test, alpha = 0.05, beta = 0.9). Our system yields statistically robust results from light micrographs. In future, it is hoped that this system will substitute for the expensive and time-consuming analysis of spinal cord injury at the ultra-structural level, such as by manual interpretation of nonoverlapping electron micrographs.