The locations and distribution of cell types in the brain, can be analyzed with Neurolucida, NeuroInfo, and BrainMaker. Researchers can map the distributions of a particular cell type, like those producing parvalbumin for example, and obtain analyses such as the nearest neighbor analysis to determine the distance from one cell to another or the distance from the cells to an anatomical boundary. 

Recent advances in molecular neuroanatomical tools have expanded the ability to map connections of specific neuron subtypes in the context of behaviorally driven patterns of neuronal activity. Analysis of such data across the whole mouse brain, registered to a reference atlas, aids in understanding the functional organization of brain circuits related to behavior. NeuroInfo works on mouse brain sections labeled with standard histochemical techniques, reconstructs those images into a whole brain image volume and registers those images to the Allen Mouse Brain Atlas. Image detection of cells and quantification of axon density labeling are then combined with the structures in the annotated reference atlas. Examples of these analyses include mapping the axonal projections of layer‐specific cortical neurons using Cre‐dependent AAV vectors and for mapping inputs to such neurons using retrograde transsynaptic tracing with modified rabies viral vectors.

The neurons comprising many brain areas are known to be arranged topographically such that nearby neurons have receptive fields at nearby locations in the brain. The anatomical overlap of terminal arborizations often corresponds to shared targeting of functional synaptic output to specific single neurons. NeuroInfo uses a methodology to quantitatively compare projections from different injections sites.