morph_stats: morphometric statistics extractionΒΆ
The morph_stats
application extracts morphometrics from a set of neuron morphology
files and produces a summary in JSON or CSV format. It may obtain any of the morphometrics available
in the neurom.get()
function, and is highly configurable, allowing the user to get
raw or summary statistics from a large set of neurite and neuron features.
The functionality can be best explained by looking at a sample configuration file:
neurite:
section_lengths:
- max
- total
section_volumes:
- total
section_branch_orders:
- max
neurite_type:
- AXON
- APICAL_DENDRITE
- BASAL_DENDRITE
- ALL
neuron:
soma_radii:
- mean
Here, there are two feature categories,
neurite
: these are morphometrics obtained from neurites, e.g. branch orders, section lengths, bifurcation angles, path lengths.neuron
: these are morphometrics that can be applied to a whole neuron, e.g. the soma radius, the trunk radii, etc.
Each category sub-item (section_lengths, soma_radii, etc) corresponds to a
neurom.get()
feature, and each one of its sub-items corresponds to a statistic, e.g.
raw
: array of raw valuesmax
,min
,mean
,median
,std
: self-explanatory.total
: sum of the raw values
An additional field neurite_type
specifies the neurite types into which the morphometrics
are to be split. This is a sample output using the above configuration:
{
"some/path/morph.swc":{
"mean_soma_radius":0.17071067811865476,
"axon":{
"total_section_length":207.87975220908129,
"max_section_length":11.018460736176685,
"max_section_branch_order":10,
"total_section_volume":276.73857657289523
},
"all":{
"total_section_length":840.68521442251949,
"max_section_length":11.758281556059444,
"max_section_branch_order":10,
"total_section_volume":1104.9077419665782
},
"apical_dendrite":{
"total_section_length":214.37304577550353,
"max_section_length":11.758281556059444,
"max_section_branch_order":10,
"total_section_volume":271.9412385728449
},
"basal_dendrite":{
"total_section_length":418.43241643793476,
"max_section_length":11.652508126101711,
"max_section_branch_order":10,
"total_section_volume":556.22792682083821
}
}
}
For more information on the application and available options, invoke it with the --help
or -h
option.
morph_stats --help