Library for manipulating neuromorpho resources.
Project description
neuromorpholib
Installation
pip3 install neuromorpholib
Usage
Downloading
A simple download of known dataset and name
from neuromorpholib import neuromorpho
nmo = neuromorpho.NeuroMorpho()
acc1 = nmo.download_swc("martone", "ACC1")
A query for all species=mouse neurons
mouse_neurons = nmo.search({"species": "mouse"})
Download a SWC for a mouse neuron
swc_demo = nmo.download_swc(
mouse_neurons[0]
)
If you know the archive name and neuron name, you can also download the swc directly by passing archive
and neuron_name
arguments.
If you only want the SWC text and don't want it to be converted into a NeuronMorphology
object, you can pass text_only=True
.
SWC Management
Read a SWC file from disk
from neuromorpholib.swc import load_swc, NeuronMorphology
my_morphology = load_swc("my_neuron.swc")
# This is a NeuronMorphology object.
Get a list of branch points
branch_points = my_morphology.get_branch_points()
Get a simplified graph (only leaves and branch points) of a morphology
morphology_graph = my_morphology.smoothed()
# nx.DiGraph
SWC Geometry Operations
Rotate, translate, or scale a geometry with NeuronMorphology
functions:
n = NeuronMorphology()
n.scale(3)
n.translate([4, 44, 10])
n.rotate([0, 0, math.pi/2])
Project details
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Source Distribution
neuromorpholib-0.2.0.tar.gz
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