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: add_barrel_annotations.py Python script to add barrel annotations to the annotations file from CCFv3. annotation_barrels.feather Table for barrel annotations, with voxel positions, flat positions, layers and hemisphere information. annotation_barrels.nrrd Annotation of individual barrels and barrel columns per layer. depth.nrrd Streamline-derived absolute cortical depth in µm. flatmap.nrrd Mapping of voxel centers in a single hemisphere to 2D coordinates in the range X,Y=[0,1]. flatmap_both.nrrd Mapping of voxel centers in both hemispheres to 2D coordinates in the range X=[0,2], Y=[0,1]. flatplot.py Python script to plot volumetric data in flat space (flat view), using the package datashader. hierarchy.json Region hierarchy in AIBS format extended with barrel annotations. thickness.nrrd Streamline-derived cortical thickness in µm. Add barrel annotations to CCFv3 Requires data file annotation_10.nrrd from CCFv3 release and Python package voxcell. The script introduces annotations of individual barrels and barrel columns (split per layer) in the SSp-bfd region. The input files are the 10 µm annotation volume from CCFv3, and the provided barrel_annotations.nrrd. The output is consistent with the provided extended hierarchy file hierarchy.json. python add_barrel_annotations.py annotation_10.nrrd annotation_barrels.nrrd annotation_barrels_10.nrrd Generate flat views of volumetric data The provided script flatplot.py requires the following Python packages: voxcell, datashader, colorcet, seaborn (optional). For example, to generate a flat view of mean cortical thickness, run the following command: python flatplot.py --autospan -r mean -c sns:viridis flatmap_both.nrrd thickness.nrrd thickness Enhanced atlas and flatmap of P14 rat somatosensory cortex Contents of rat_sscx_enhanced.zip: brain_regions.nrrd Region annotations for rat somatosensory cortex. example.py Example Python script for loading and analyzing atlas datasets, using the package voxcell. flatmap.nrrd Mapping of voxel centers to flat 2D coordinates in the range X,Y=[0,1]. hexgrid.nrrd Decomposition of somatosensory cortex into 263 hexagonal columns of approximately 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]. shells.nrrd Boundaries of somatosensory cortex (top, bottom, sides). thickness.nrrd Cortical thickness in µm. Together, relative depth and flat coordinates make a 3D coordinate system adapted to the shape of the somatosensory 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.