API Reference

• Command Line Utilities (skeleton_keys.cmds)
  • skelekeys-layer-aligned-swc
  • skelekeys-upright-corrected-swc
  • skelekeys-profiles-from-swcs
  • skelekeys-calc-histogram-loadings
  • skelekeys-morph-features
  • skelekeys-postprocess-features
  • skelekeys-layer-aligned-coords
  • skelekeys-profiles-from-coords
• Database Queries (skeleton_keys.database_queries)
  • Queries with default engine
  • Queries with specified engine
  • Query Engine
• Depth Profile Features (skeleton_keys.depth_profile)
  • skeleton_keys.depth_profile.calculate_pca_transforms_and_loadings
  • skeleton_keys.depth_profile.apply_loadings_to_profiles
  • skeleton_keys.depth_profile.earthmover_distance_between_compartments
  • skeleton_keys.depth_profile.overlap_between_compartments
• Layer Drawings (skeleton_keys.drawings)
  • skeleton_keys.drawings.snap_hand_drawn_polygons
  • skeleton_keys.drawings.convert_and_translate_snapped_to_microns
• Feature Definition (skeleton_keys.feature_definition)
  • skeleton_keys.feature_definition.default_features
• Input/Output (skeleton_keys.io)
  • SWC files
  • Reference information
  • Saving internal database information to files
• Layer Alignment (skeleton_keys.layer_alignment)
  • skeleton_keys.layer_alignment.layer_aligned_y_values
  • skeleton_keys.layer_alignment.layer_aligned_y_values_for_morph
  • skeleton_keys.layer_alignment.cortex_thickness_aligned_y_values
  • skeleton_keys.layer_alignment.cortex_thickness_aligned_y_values_for_morph
  • skeleton_keys.layer_alignment.fractions_within_layer
  • skeleton_keys.layer_alignment.step_all_nodes
  • skeleton_keys.layer_alignment.layer_side_depths
  • skeleton_keys.layer_alignment.layer_locations
  • skeleton_keys.layer_alignment.setup_interpolator_without_nan
  • skeleton_keys.layer_alignment.path_dist_from_node
  • skeleton_keys.layer_alignment.calculate_length_of_path_list
• Plotting (skeleton_keys.plotting)
  • skeleton_keys.plotting.plot_cortical_cell
  • skeleton_keys.plotting.plot_layer_polygon
• Slice Angle (skeleton_keys.slice_angle)
  • skeleton_keys.slice_angle.slice_angle_tilt
• Uprighting Morphologies (skeleton_keys.upright)
  • skeleton_keys.upright.upright_corrected_morph
  • skeleton_keys.upright.corrected_without_uprighting_morph