ccf_streamlines.morphology.transform_swc_to_volume#

ccf_streamlines.morphology.transform_swc_to_volume(swc_file, volume_shape=(1320, 800, 1140), resolution=(10, 10, 10), compartments=None)#

Create a volume with node counts from a morphology SWC file.

Parameters

  • swc_file (str) – File path of SWC file

  • volume_shape (3-tuple of ints, default (1320, 800, 1140)) – Shape of target volume in voxels

  • resolution (3-tuple of ints, default (10, 10, 10)) – Size of voxels in microns

  • compartments (list-like, optional) – List of compartment types to include 1 = soma 2 = axon 3 = basal dendrite (or generic dendrite) 4 = apical dendrite If None (default), all compartments are included.

Returns

volume – Volume with shape volume_shape with counts of nodes in each voxel

Return type

array