This map features pathway reconstructions of tracer-labeled connections from the entire cortex to the amygdala.


This cortico-cortical map provides an overview of projection patterns for each cortical injection case available in iConnectome. Data were manually reconstructed from raw images--axons appear as shaded regions and retrogradely labeled cells appear as colored dots. A large dot indicates injection site.


This map contains reconstructions of cortico-striatal projections generated with threshold-based reconstruction algorithm that segments axons labeled by anterograde tracers from tissue background. Only terminal fields within the caudoputamen are depicted. Raw tracer data for all mapped cases are available on iConnectome.

Dynamic Caudoputamen (CP)

This dynamic map provides a list of all cortical areas that primarily project to each of the domains within the rostral, intermediate, and caudal CP (or dorsal striatum). The data is based on the quantification of 62 tracer-labeled cortico-striatal pathways. A community detection algorithm was applied to the quantified data to cluster cortical tracer injection sites with common CP termination fields across the CP. Subsequent centroid analyses extracted smaller clusters of projection fields, or domains, within the communities. A total of 29 distinct striatal domains were identified based on their cortical afference [for more details, please see Hintiryan, Foster et al., (2016). The mouse cortico-striatal projectome].

A comprehensive map featuring all projection pathways originating from the cortex to the brain stem. Raw images for the cases can be found in iConnectome.