Cell Annotation Software was designed for neuroscience research by researchers specializing in an image processing domain. It is a result of a collaboration between the Silesian University of Technology, Poland (Karolina Nurzynska, Ph.D.), AGH University of Science and Technology, Poland (Adam Piorkowski, Dsc Ph.D.), and Pavlov Institute of Physiology RAS, Russia (Aleksandr Mikhalkin). The program was developed in order to facilitate the analysis of microscopic images of nuclei data gathered with various settings of experiments, resulting in greyscale and color images. The main functionality of the system consists on cell border detection. Additionally, it allows to divide the cells into regions, calculate features, which describe the cell shape. If necessary it is possible to manually adjust each cell shape or remove it from further processing. Since this is a trial version it is still improved.