Enhanced atlases and flatmaps of rodent neocortex

<strong>Enhanced atlas and flatmap of P14 rat somatosensory cortex</strong> Contents of rat_sscx_enhanced.zip: <strong>brain_regions.nrrd</strong> Region annotations for rat somatosensory cortex. <strong>example.py</strong> Example python script for loading and analyzing atlas datasets, using the package voxcell. <strong>flatmap.nrrd</strong> Mapping of voxel centers to flat 2D coordinates in the range [0,1]. <strong>hexgrid.nrrd</strong> Decomposition of somatosensory cortex into 263 hexagonal columns of approximately equal size. <strong>hierarchy.json</strong> Region hierarchy in AIBS format. <strong>orientation.nrrd</strong> Local orientation towards pia, stored as a quaternion. <strong>relative_depth.nrrd</strong> Relative cortical depth in the range [0,1]. <strong>shells.nrrd</strong> Boundaries of somatosensory cortex (top, bottom, sides). <strong>thickness.nrrd</strong> Cortical thickness in µm. Together, relative depth and flat coordinates make a 3D coordinate system adapted to the shape of the cortex. The principal axis (local orientation) is orthogonal to layer boundaries, and the remaining two axes span the flat space and are locally orthogonal to the principal axis.