The ancient Egyptians thought of the brain as a stuffing for the skull and Aristotle considered it to be a blood-cooling organ - such beliefs were changed by classical neuroscience in such a way that typical characteristics of the heart such as personality, intelligence and mind were assigned to the brain as the new central organ of the human body. On the other hand, modern neuroscience began with Santiago Ramón y Cajal’s hypothesis in the late 19th century that the brain is made up of individual cells that communicate with each other and the small protrusions of these cells that he previously observed served as potential mediators of such connections. Although he could not prove his assumptions due to the limited technological possibilities of his time, to this day most have been proved correct and dendritic spines have become central structures of basic brain processes such as learning and memory. Spines have been found to occur in a variety of sizes and shapes and to be prone to change of their shape, but also to easily form and disappear from dendrites. Such dynamic changes have become fertile ground for research into the learning and memory process because the success of memorisation has been associated with changes in the size of individual spines. From such a connection between morphology and function, active studies of the morphometry of spines began to explain their functional aspects. Besides, quantitative changes at the population or individual spine level have been identified as a potential structural basis for symptoms in neuropsychiatric disorders. Due to the resolution limitations of classical visualisation methods, modern research is focused on the development of nanoresolution imaging methods to make morphometric measurements credible and to allow valuable conclusions to be drawn from the analysis of the results. The problems of most existing imaging methods are performance difficulties and high cost and quantitative analyses of morphometric values are time-consuming, extremely complex and require extensive user intervention because there is still no quality software tool to completely automate such analyses.