skeleton_keys.upright.upright_corrected_morph#

skeleton_keys.upright.upright_corrected_morph(morphology, upright_angle, slice_angle, flip_status, shrink_factor)#

Rotate morphology upright and correct for shrinkage and slice angle

Parameters:

  • morphology (Morphology) – Original morphology (micron scale, in image alignment)

  • upright_angle (float) – Angle to rotate to upright the morphology (radians)

  • slice_angle (float) – Angle between actual slice and plane parallel to streamlines (radians)

  • flip_status (integer) – 1 = slice was flipped before recording; -1 = slice was not flipped

  • shrink_factor (float) – Factor to multiple z-values by to correct for slice shrinkage

Returns:

corrected_morph – Morphology in upright orientation after correcting for shrinkage and slice angle

Return type:

Morphology