Fig. 1

Quantification of CLARITY imaging. a Sections of DTI-scanned brain were segmented at different bregma levels for (i) the orbitofrontal cortex, (ii) the anterior hippocampus and amygdala, (iii) the mid hippocampus and posterior amygdala and (iv) the posterior hippocampus. b–d DTI-scanned brains were computed for tracts. Tissue from wild-type and Nrxn2α KO mice were cleared and stained for neurofilament and DAPI (e). f Automated MATLAB scripts were used to segment the DAPI (blue) and neurofilament (purple) channels such that cell density and axonal density and orientation could be calculated. g is representative of a CLARITY-derived 3D stacked image of a DAPI and neurofilament of a region of interest, with h being the corresponding segmented image. Scale bar, 100 μm