Before revision:  We show registration results for Nissl, myelin, CTB, and fluorescent tracer images using a same-subject ex-vivo MRI as our reference and show that our method achieves accurate registration and eliminates artifactual warping that may be result from the absence of a reference MRI data set. Examination of the determinant of the local metric tensor of the diffeomorphic mapping between each subject's ex-vivo MRI and resultant Nissl reconstruction allows an unprecedented local quantification of geometrical distortions resulting from the histological processing, showing a slight shrinkage, a median linear\pm  scale change of ~-1\% in going from the ex-vivo MRI to the tape-transfer generated histological image data\pm  .
After revision:  We quantify the scale change during the different stages of histological processing of the brains using the Jacobian determinant of the local metric tensor of the diffeomorphic mapping between each subject's ex-vivo MRI and resultant Nissl reconstruction allows an unprecedented local quantification of geometrical distortions resulting from the histological processing, showing a slight shrinkage, a median linear\pm scale change of ~-1\% in going from the ex-vivo MRI to the tape-transfer generated histological image data\pm .