skeleton_keys.database_queries.shrinkage_factor_from_database#

skeleton_keys.database_queries.shrinkage_factor_from_database(morph, specimen_id, cut_thickness=350.0)#

Determine shrinkage factor for morphology using database information

Parameters:

  • morph (Morphology) – Neuronal morphology

  • cut_thickness (float, default 350.) –

  • specimen_id (int) – Specimen ID

  • cut_thickness – The cutting thickness (in microns) of the original slice. Used as an upper limit to the calculated thickness or as a fallback value if the thickness cannot be determined from the morphology and markers.

Returns:

corrected_scale – The factor to multiply the z-dimension by to adjust for shrinkage

Return type:

float