Enhanced atlases and flat maps of rodent neocortex

Enhanced atlas and flat map of P14 rat somatosensory cortex Contents of rat_sscx_enhanced.zip: brain_regions.nrrd Region annotations for rat somatosensory cortex. hierarchy.json Region hierarchy in AIBS format. relative_depth.nrrd Relative cortical depth in [0,1]. thickness.nrrd Cortical thickness in µm. orientation.nrrd Local orientation towards pia, stored as a quaternion. flatmap.nrrd Mapping of voxel centers to 2D coordinates in [0,1] (flat space). hexgrid.nrrd Decomposition of somatosensory cortex into 263 hexagonal columns of approximately equal size. example.py Example python script for loading and analyzing atlas datasets, using the package voxcell. 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.