NeuroM: a light-weight neuron morphology analysis package
Project description
NeuroM is a Python-based toolkit for the analysis and processing of neuron morphologies.
Acknowlegments
This work has been partially funded by the European Union Seventh Framework Program (FP7/2007�2013) under grant agreement no. 604102 (HBP). For license and authors, see LICENSE.txt and AUTHORS.md respectively.
Documentation
NeuroM documentation is built and hosted on readthedocs.
Dependencies
The build-time and runtime dependencies of NeuroM are:
numpy
scipy
matplotlib
h5py (optional, required for reading HDF5 files)
enum34 (pip install takes care of this)
pyyaml (pip install takes care of this)
Installation
It is recommended that you use pip to install into NeuroM into a virtualenv:
NeuroM installation
The following assumes virtualenv named nrm with access to the dependencies has been set up and activated. We will see two ways to install NeuroM
From the Python Package Index
From the git repository
From source (for NeuroM developers)
Install package from Python Package Index
(nrm)$ pip install neuromInstall package from git
Install the latest version:
(nrm)$ pip install git+https://github.com/BlueBrain/NeuroM.gitInstall a particular release:
(nrm)$ pip install git+https://github.com/BlueBrain/NeuroM.git@neurom-v0.0.1Install from source
Clone the repository and install it:
(nrm)$ git clone https://github.com/BlueBrain/NeuroM.git
(nrm)$ pip install -e ./NeuroMThis installs NeuroM into your virtualenv in “editable” mode. That means changes you make to the source code are seen by the installation. To install in read-only mode, omit the -e.
Examples
Perform checks on neuron morphology files:
(nrm)$ morph_check some/data/path/morph_file.swc # single file
INFO: ================================
INFO: Check file some/data/path/morph_file.swc...
INFO: Has valid soma? PASS
INFO: Has Apical Dendrite? PASS
INFO: Has Basal Dendrite? PASS
INFO: All neurites have non-zero radius? PASS
INFO: All segments have non-zero length? PASS
INFO: All sections have non-zero length? PASS
INFO: Check result: PASS
INFO: ================================
(nrm)$ morph_check some/data/path # all files in directory
....Load a neuron and obtain some information from it:
>>> from neurom import ezy
>>> nrn = ezy.load_neuron('some/data/path/morph_file.swc')
>>> apical_seg_lengths = ezy.get('segment_lengths', nrn, neurite_type=ezy.NeuriteType.apical_dendrite)
>>> axon_sec_lengths = ezy.get('section_lengths', nrn, neurite_type=ezy.NeuriteType.axon)Visualize a neuronal morphology:
>>> # Initialize nrn as above
>>> from neurom import viewer
>>> fig, ax = viewer.draw(nrn)
>>> fig.show()
>>> fig, ax = viewer.draw(nrn, mode='3d') # valid modes '2d', '3d', 'dendrogram'
>>> fig.show()Release history Release notifications | RSS feed
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