Enhanced atlases and flatmaps of rodent neocortex

Flatmap of mouse isocortex and barrel column annotations in CCFv3 space (10 µm resolution) Contents of mouse_isocortex_enhanced.zip: annotation_barrels.nrrd: Pre-generated annotations of barrel columns divided into layers, can be transplanted directly into the CCFv3 atlas. barrel_positions.feather: 3D coordinates of segmented barrel voxels used to create annotations. central-streamlines.feather: Central streamlines used to calculate barrel cortex metrics. depth.nrrd: Streamline-derived absolute cortical depth in µm. flatmap.nrrd: Mapping of voxels in a single hemisphere to 2D coordinates in the range X,Y=[0,1]. flatmap_both.nrrd: Mapping of voxels in both hemispheres to 2D coordinates in the range X=[0,2], Y=[0,1]. hexgrid.nrrd: Decomposition of mouse isocortex into 1307 hexagonal columns of roughly equal size. hierarchy.json: Region hierarchy in AIBS format extended with barrel annotations. thickness.nrrd: Streamline-derived cortical thickness in µm. flatmap_input/Makefile: Pipeline to derive inputs to the flatmapping algorithm from CCFv3 datasets. flatmap_input/config.mk: Configuration file for the flatmapping algorithm. Enhanced atlas and flatmap of P14 rat somatosensory cortex Contents of rat_sscx_enhanced.zip: brain_regions.nrrd: Annotated regions in rat somatosensory cortex, divided into layers. flatmap.nrrd: Mapping of voxels to 2D coordinates in the range X,Y=[0,1]. hexgrid.nrrd: Decomposition of rat somatosensory cortex into 263 hexagonal columns of roughly equal size. hierarchy.json: Region hierarchy in AIBS format. orientation.nrrd: Local orientation towards pia, stored as a quaternion. relative_depth.nrrd: Relative cortical depth in the range [0,1]. thickness.nrrd: Cortical thickness in µm. flatmap_input/config.mk: Configuration file for the flatmapping algorithm. flatmap_input/annotations.nrrd: Annotations of rat somatosensory regions. flatmap_input/mask.nrrd: Labeling of source volume into interior, exterior, top/bottom/sides boundaries. flatmap_input/orientation_{x,y,z}.nrrd: Components of the orientation vector, as input to the flatmapping algorithm. flatmap_input/relative_depth.nrrd: Relative depth field, as input to the flatmapping algorithm. Code to generate barrel cortex annotations and flatmaps can be found in a software repository under a free software license.