  CLARITY is a method for converting biological tissues into translucent and
porous hydrogel-tissue hybrids. This facilitates interrogation with light sheet
microscopy and penetration of molecular probes while avoiding physical slicing.
In this work, we develop a pipeline for registering CLARIfied mouse brains to
an annotated brain atlas. Due to the novelty of this microscopy technique it is
impractical to use absolute intensity values to align these images to existing
standard atlases. Thus we adopt a large deformation diffeomorphic approach for
registering images via mutual information matching. Furthermore we show how a
cascaded multi-resolution approach can improve registration quality while
reducing algorithm run time. As acquired image volumes were over a terabyte in
size, they were far too large for work on personal computers. Therefore the
NeuroData computational infrastructure was deployed for multi-resolution
storage and visualization of these images and aligned annotations on the web.
