Script for extracting many dendritic and axonal features from SWC or ASC files using the NeuroM package
Author: René Wilbers, renewilbers@gmail.com
- Only tested with python 3.x . Needs the NeuroM package installed (https://neurom.readthedocs.io)
- Open SWC_ASC_morph_feature_analysis.py and indicate the location of input & output folders
- Make sure filenames are in the following format: [Species][xx][Layer][neuron_id], for example: HumanIN_L3_123456.SWC or MousePN_L23_123.ASC
- Run Script
- Features are exported to excel files.
- TAL/TDL/TDL_A/TDL_B --> total axonal length, total dendritic length, total dendritic length apicals, total dendritic length basals
- TAA/TDA etc --> surface area
- TAV/TDV etc --> volume
- ABP/DBP etc --> branchpoints
- leaf order --> leaf = final segment of a dendritic or axonal branch. Order depends on how often a segment has branched. So, a segment coming directly from the soma is 1st order, the segments branching from there are 2nd order, etc... Leaf order is calculated as the mean order of the leafs.
- reachvol--> volume of a polygonal 3D shape defined by the leaf endings
- DSC --> dendritic stem count. number of primary dendrites stemming from the soma
- dendpathlength --> mean path length of soma to ends of the dendrites
- dendleaflength --> segment length of the leafs (terminal segments)
- dendbranchlength --> segment length of the branches (nonterminal segments)
- dendmaxpathlength --> length of the longest path from soma to the end of a dendrite
- dendmeanbranchdiam --> mean diameter of the branches (nonterminal segments)
- dendmeanleafdiam --> mean diameter of the leafs (terminal segments)
- axstart --> indicates how far away from the soma the axon starts (if it emerges from dendrite), 0 if it emerges from soma.
- axtodend --> TDA/TAA
- dend_um_per_BP --> TDL/DBP
- axon_um_per_BP --> TAL/ABP
- axonal efficiency --> Calculated as axreachvol^(1/3) / TAL. Says something about how efficiently the axon reaches around (so large reach with small amount of cable is considered efficient).
- dendric efficiency --> Same story, but dendreachvol^(1/3) / TDL
- mean_total_stem_length --> TDL/DSC
- mean_total_stem_ branchpoints --> DBP/DSC