morph_stats: morphometric statistics extractionΒΆ
The morph_stats
application extracts morphometrics from a set of neuron morpholigy
files and produces a summary JSON output. 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_lehgths, 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