This paper presents new spatial analysis techniques in recognition and localization neural activity in the healthy mouse brain. The source materials obtained using light-sheet microscopy throughout the brain are presented as multi-page TIFF files with records of spatial brightness distribution of fluorescently activated mouse brain cells, and contain images from hundreds of slices. Main purpose of this work is to identify rapid short-term activity occurring in an environment of stable long-term activity. To improve computational operations, we divide slices in source images into layers, where each layer contains activity localizations with a set range of directions. Topological data processing is performed using QGIS applications. New approaches used in this work make it possible to determine in detail the individual reactions of mouse brain cells with reference to their localization, including cases of simultaneous reactions of different groups of neuronal cells.