ccf_streamlines.projection.IsocortexCoordinateProjector#

class ccf_streamlines.projection.IsocortexCoordinateProjector(surface_paths_file, closest_surface_voxel_reference_file, layer_thicknesses=None, streamline_layer_thickness_file=None, resolution=(10, 10, 10), projection_file=None)#

” Class for projecting CCF coordinates to flattened representation.

Can be used without a 2-D view to obtain only depth from pia values

Parameters

  • surface_paths_file (str) – File path to an HDF5 file containing information about the paths between the top and bottom of cortex.

  • closest_surface_voxel_reference_file (str) – File path to a HDF5 file containing information about the closest streamlines for voxels within the isocortex.

  • layer_thicknesses (dict, optional) – Default None. Dictionary of layer thicknesses. Only used if thickness_type in methods is normalized_layers.

  • streamline_layer_thickness_file (str, optional) – Default None. File path to an HDF5 file containing information about the layer thicknesses per streamline. Only used if thickness_type in methods is normalized_layers.

  • resolution (tuple, default (10, 10, 10)) – 3-tuple of voxel dimensions in microns

  • projection_file (str, optional) – File path to an HDF5 file containing the 2D projection information. If None (default), only depth information can be obtained.

__init__(surface_paths_file, closest_surface_voxel_reference_file, layer_thicknesses=None, streamline_layer_thickness_file=None, resolution=(10, 10, 10), projection_file=None)#

Methods

__init__(surface_paths_file, ...[, ...])

project_coordinates(coords[, scale, ...])

Project set of coordinates to the flattened slab

project_depths(coords[, thickness_type, scale])

Determine depths of set of CCF coordinates

Attributes

ISOCORTEX_LAYER_KEYS