sCRACM relies on photostimulating axons, which can JAK inhibitor be efficiently excited even when severed from their parent somata.
Therefore, sCRACM can map connections between defined neuronal populations over long length scales, not limited to circuits preserved in brain slices. sCRACM also provides an estimate of the spatial distribution of synapses made by ChR2-positive axons onto the dendritic arbors of recorded neurons. Here, we applied anatomical methods and sCRACM to map inputs from vS1 onto neurons in vM1. vM1 neurons in upper layers (L2/3 and L5A), which harbor mostly cortico-cortical neurons, receive strong input from vS1. These neurons also provide the majority of the projection back to vS1. In contrast, deep layer neurons (L5B and
L6), which include the “corticofugal” neurons that project to motor centers in the brainstem and elsewhere, received only weak input from vS1. We characterized the projections EGFR inhibitor between vibrissal somatosensory cortex (vS1) and vibrissal motor cortex (vM1) using viral-mediated anterograde tracing (Figure 1; see Figure S1 and Movie S1 available online). vS1 was identified by the presence of large barrels. vS1 layers were defined according to well-established cytoarchitectural criteria (Bureau et al., 2006 and Groh et al., 2010). Individual layers contain distinct sets of neurons, with different projection patterns and inputs (Groh et al., 2010, Hattox and these Nelson, 2007, Sato and Svoboda, 2010 and Svoboda et al., 2010). We labeled vS1 neurons by
infection with recombinant adeno-associated viruses (AAV) (Chamberlin et al., 1998) expressing eGFP or tdTomato, and imaged the projections of the infected neurons throughout the brain using a high-resolution slide scanner (excluding most of brainstem and spinal cord). Infected neurons were distributed over several barrel columns (diameter of infection site <1.5 mm) (Figures 1A and 1B), mainly in L2/3 and L5 (Figure S1A). Axonal projections were seen in multiple cortical and subcortical targets. We quantified these projections by integrating the fluorescence intensity over the sections containing specific targets and fluorescent axons (see Supplemental Experimental Procedures).