Title: Joint Atlas-Mapping of Multiple Histological Series combined with Multimodal MRI of Whole Marmoset Brains,
Abstract: Development of a mesoscale neural circuitry map of the common marmoset is an
essential task due to the ideal characteristics of the marmoset as a model
organism for neuroscience research. To facilitate this development there is a
need for new computational tools to cross-register multi-modal data sets
containing MRI volumes as well as multiple histological series, and to register
the combined data set to a common reference atlas. We present a fully automatic
pipeline for same-subject-MRI guided reconstruction of image volumes from a
series of histological sections of different modalities, followed by
diffeomorphic mapping to a reference atlas. 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 scale change of ~-1% in going from the
ex-vivo MRI to the tape-transfer generated histological image data.