There is another thread about aligning MERFISH data to spatial locations here.
If you’d like to see where cell types are expressed in the brain in the mouse whole brain data hosted at Allen Brain Map, you could (1) visualize data on the ABC Atlas or (2) see top brain regions per cell type using Annotation Comparison Explorer in this configuration:
There currently is no direct way to align MapMyCells output (which is based on cell types) to specific anatomic structures.