ABSTRACT
Light-sheet microscopy has emerged as the method of choice to perform brain studies the at whole-organ scale. The brain is an extremely complex organ, whose structure and function spans many orders of magnitude. Single-cell mapping in entire cleared mouse brain is particularly suited to investigate whole-brain behavior-specific neuronal activation by looking at the expression of immediate early genes. Investigating the subtle interaction between brain structure and function thus requires the ability to map large volumes with high spatial resolution and substantial speed. BrainCellFinder has enabled a thorough analysis of the spatial distribution of Purkinje cells in the mouse cerebellum. On a wider scale, Renier and co-authors developed ClearMap, a tool for brain-wide analysis of cells labeled through immunohistochemistry. This software includes both a 3D registration step to align the acquired volume onto a reference atlas, and a cell detection step based on image filtering and peak detection.
