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skeleton_keys 0.1.1 documentation

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  • Installation
  • User’s Guide
  • API Reference

Site Navigation

  • Installation
  • User’s Guide
  • API Reference

Section Navigation

  • Command Line Utilities ( skeleton_keys.cmds )
    • skeleton_keys.cmds.layer_aligned_swc.LayerAlignedSwcSchema
    • skeleton_keys.cmds.upright_corrected_swc.UprightCorrectedSwcSchema
    • skeleton_keys.cmds.upright_corrected_swc.soma_distance_from_pia
    • skeleton_keys.cmds.depth_profiles_from_aligned_swcs.ProfilesFromAlignedSwcsParameters
    • skeleton_keys.cmds.calc_histogram_loadings.CalcHistogramLoadingsParameters
    • skeleton_keys.cmds.process_morphology_features.ProcessMorphologyFeaturesParameters
    • skeleton_keys.cmds.process_morphology_features.soma_locations
    • skeleton_keys.cmds.process_morphology_features.select_and_convert_depth_columns
    • skeleton_keys.cmds.process_morphology_features.analyze_depth_profiles
    • skeleton_keys.cmds.process_morphology_features.specimen_morph_features
    • skeleton_keys.cmds.postprocess_features.PostprocessFeaturesParameters
    • skeleton_keys.cmds.layer_aligned_coords.LayerAlignedCoordsSchema
    • skeleton_keys.cmds.depth_profiles_from_aligned_coords.ProfilesFromAlignedCoordsParameters
  • Database Queries ( skeleton_keys.database_queries )
    • skeleton_keys.database_queries.swc_paths_from_database
    • skeleton_keys.database_queries.pia_wm_soma_from_database
    • skeleton_keys.database_queries.shrinkage_factor_from_database
    • skeleton_keys.database_queries.layer_polygons_from_database
    • skeleton_keys.database_queries.determine_flip_switch
    • skeleton_keys.database_queries.query_for_swc_file
    • skeleton_keys.database_queries.query_for_image_series_id
    • skeleton_keys.database_queries.query_for_cortical_surfaces
    • skeleton_keys.database_queries.query_for_layer_polygons
    • skeleton_keys.database_queries.query_for_soma_center
    • skeleton_keys.database_queries.query_marker_file
    • skeleton_keys.database_queries.query_cell_depth
    • skeleton_keys.database_queries.query_pinning_info
    • skeleton_keys.database_queries.default_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 )
    • skeleton_keys.io.load_swc_as_dataframe
    • skeleton_keys.io.load_default_layer_template
    • skeleton_keys.io.save_lims_surface_and_layers_to_json
  • 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

Uprighting Morphologies (skeleton_keys.upright)#

Functions related to adjusting the rotation of morphologies so that the direction to the pia is up (positive y-axis) and the direction to the white matter is down (negative y-axis).

upright.upright_corrected_morph(morphology, ...)

Rotate morphology upright and correct for shrinkage and slice angle

upright.corrected_without_uprighting_morph(...)

Correct for shrinkage and slice angle without uprighting

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© Copyright 2022, Nathan Gouwens, Forrest Collman, Matt Mallory, Clare Gamlin.

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