Enhanced atlases and flatmaps of rodent neocortex

Flatmaps of mouse isocortex and barrel column annotations in CCFv3 space (10 µm resolution)

• 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_authalic_shaped_256.nrrd: Discretized flatmap for use in flatmap comparison notebook (256x256 pixel resolution, shape-match border).
  
• flatmap_authalic_square_256.nrrd: Discretized flatmap for use in flatmap comparison notebook (256x256 pixel resolution, square border).
• flatmap_both_shaped.nrrd: Flatmap of mouse isocortex in both hemispheres (shape-match border).
• flatmap_both_square.nrrd: Flatmap of mouse isocortex in both hemispheres (square border).
• flatmap_shaped.nrrd: Flatmap of mouse isocortex in a single hemisphere (shape-match border).
• flatmap_square.nrrd: Flatmap of mouse isocortex in a single hemisphere (square border).
• 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.
• isocortex.nrrd: Annotations of mouse isocortex regions in a single hemisphere (1-based, consecutive) for plotting in ITK-SNAP.
• isocortex.label: Accompanying label file for plotting isocortex.nrrd in ITK-SNAP.
• thickness.nrrd: Streamline-derived cortical thickness in µm.
• flatmap_input/Makefile: Pipeline to derive inputs for the flatmapping algorithm from CCFv3 datasets.
• flatmap_input/border_points.txt: Border points for the shape-match flatmap, a convex approximation to the shape of the CCFv3 flatmap.
• flatmap_input/config_shaped.mk: Configuration file for the flatmapping algorithm (shape-match border).
• flatmap_input/config_square.mk: Configuration file for the flatmapping algorithm (square border).

Enhanced atlas and flatmap of P14 rat somatosensory cortex

• brain_regions.nrrd: Annotated regions in rat somatosensory cortex, divided into layers.
• flatmap.nrrd: Flatmap of rat somatosensory cortex in a single hemisphere (square border).
• 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].
• sscx.nrrd: Annotations of rat somatosensory cortex regions in a single hemisphere (1-based, consecutive) for plotting in ITK-SNAP.
• sscx.label: Accompanying label file for plotting sscx.nrrd in ITK-SNAP.
• thickness.nrrd: Cortical thickness in µm.
• flatmap_input/config.mk: Configuration file for the flatmapping algorithm.
• flatmap_input/annotations.nrrd: Annotations of rat somatosensory cortex regions (0-based, consecutive).
• 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 flatmaps and barrel cortex annotations can be found in a software repository under a free software license.