unravel.coordinates.physical_points_add_regions module#
Use coords_physical_points_add_regions or ppar from UNRAVEL to add atlas region IDs and region metadata to a CSV containing physical-space point coordinates.
This is useful when point coordinates are in physical units, e.g. µm, rather than voxel/index space. Coordinates are converted to voxel indices using the provided spacing, then atlas IDs are looked up directly from an atlas image.
- Input:
CSV with physical coordinate columns, e.g. channel_ml, channel_dv, channel_ap
Atlas image in the same array orientation as the coordinate columns
Region info CSV, e.g. CCFv3-2020_info.csv
- Output:
- CSV with original metadata plus:
x, y, z Region_ID atlas_lookup_status abbreviation full_structure_name
Note
- Coordinates are assumed to be in the same axis order as the atlas image:
x -> atlas axis 0 y -> atlas axis 1 z -> atlas axis 2
- For Kevin’s CCF-space images, this appeared to work:
x = channel_ml y = channel_dv z = channel_ap
Points outside atlas bounds are retained but assigned Region_ID = 0.
Usage:#
- coords_physical_points_add_regions
-i ISOTRP_all_recordings_units_CCFcoordinates.csv -a CCF25/atlas_CCFv3_2020_25um_in_kevin_space.nii.gz -x channel_ml -y channel_dv -z channel_ap -s 25 -csv CCFv3-2020_info.csv -id lowered_ID -o units_with_regions.csv
Usage example for one recording:#
- coords_physical_points_add_regions
-i ISOTRP_all_recordings_units_CCFcoordinates.csv -a CCF25/atlas_CCFv3_2020_25um_in_kevin_space.nii.gz -x channel_ml -y channel_dv -z channel_ap -s 25 -f “recording_name == ‘NP09_R1’” -csv CCFv3-2020_info.csv -id lowered_ID -o NP09_R1_units_with_regions.csv