Command Line Utilities (skeleton_keys.cmds)#

These command line utility scripts are designed to be used together to create a morphology feature processing pipeline.

You can access information about the arguments for each script by passing the --help option on the command line.

skelekeys-layer-aligned-swc#

Script to generate a layer-aligned SWC file.

layer_aligned_swc.LayerAlignedSwcSchema(*[, ...])

This schema is designed to be a schema_type for an ArgSchemaParser object

skelekeys-upright-corrected-swc#

Script to generate an upright, slice angle-corrected SWC file (but without layer alignment).

upright_corrected_swc.UprightCorrectedSwcSchema(*)

This schema is designed to be a schema_type for an ArgSchemaParser object

upright_corrected_swc.soma_distance_from_pia(...)

Calculate the distance (in microns) from the soma to the pia

skelekeys-profiles-from-swcs#

Script to calculate layer-aligned depth profile histograms from a set of SWC files.

depth_profiles_from_aligned_swcs.ProfilesFromAlignedSwcsParameters(*)

This schema is designed to be a schema_type for an ArgSchemaParser object

skelekeys-calc-histogram-loadings#

Script to calculate the PCA loadings for a set of layer-aligned depth profile histograms.

calc_histogram_loadings.CalcHistogramLoadingsParameters(*)

This schema is designed to be a schema_type for an ArgSchemaParser object

skelekeys-morph-features#

Script to calculate morphological features for a set of SWC files.

process_morphology_features.ProcessMorphologyFeaturesParameters(*)

This schema is designed to be a schema_type for an ArgSchemaParser object

process_morphology_features.soma_locations(df)

Obtain soma locations from DataFrame

process_morphology_features.select_and_convert_depth_columns(df, ...)

Select columns from depth profile DataFrame with particular prefix

process_morphology_features.analyze_depth_profiles(df, ...)

process_morphology_features.specimen_morph_features(...)

skelekeys-postprocess-features#

Script to perform postprocessing on the long-form morphology feature files (convert to wide format and perform z-score normalization).

When this script normalizes the values, it normalizes all the values with the same feature name to the same scale. This means that, for example, the feature extent will be normalized in both x and y dimensions (i.e., width and height) with the same scale. The intention is to avoid overemphasizing differences in particular dimensions where slight differences may not be relevant.

postprocess_features.PostprocessFeaturesParameters(*)

This schema is designed to be a schema_type for an ArgSchemaParser object

skelekeys-layer-aligned-coords#

Script to layer-aligned coordinates from a general CSV file.

layer_aligned_coords.LayerAlignedCoordsSchema(*)

This schema is designed to be a schema_type for an ArgSchemaParser object

skelekeys-profiles-from-coords#

Script to calculate layer-aligned depth profile histograms from a CSV with layer-aligned coordinates.

depth_profiles_from_aligned_coords.ProfilesFromAlignedCoordsParameters(*)

This schema is designed to be a schema_type for an ArgSchemaParser object