Abstract
CNS injuries are associated with profound changes in cell organization. This protocol presents a stepwise approach to quantitatively describe the spatiotemporal changes in glial cell rearrangement in the injured murine brain, which is applicable to other biological contexts. Herein, we apply common immunolabeling of neurons and glial cells and wide-field microscopy imaging. Then, we employ computational tools for alignment to the Allen Brain Atlas, unbiased/automatic detection of cells, generation of point patterns, and data analysis. For complete details on the use and execution of this protocol, please refer to Manrique-Castano et al.(1).