Modern research is aimed at detailed understanding of structure of the brain and its functional parts, analysis of the brain network, study of brain activity in response to various events, spontaneous activity and activity at restful state. The resolution and quality of source materials are improving, while at the same time the volume of processed data is rapidly growing, and the requirements for processing speed are increasing. One of the developing methods for obtaining data on the activation of healthy mouse brain cells is fluorescence microscopy. This technology allows brain cells to be illuminated based on their current state and records of 3D brain data sets as 2D slices. In our work, we applied geoprocessing methods to analysis of spontaneous short-term activity of mouse brain. To improve computational operations, we divide slices in source images into layers, where each layer contains activity localizations with a set range of directions.