NeuroM is a Python-based toolkit for the analysis and processing of neuron morphologies.

NeuroM documentation is built and hosted on readthedocs.

• latest snapshot
• latest release

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)

It is recommended that you use pip to install into NeuroM into a virtualenv:

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

1. From the Python Package Index
2. From the git repository
3. From source (for NeuroM developers)

(nrm)$ pip install neurom

Install the latest version:

(nrm)$ pip install git+https://github.com/BlueBrain/NeuroM.git

Install a particular release:

(nrm)$ pip install git+https://github.com/BlueBrain/NeuroM.git@neurom-v0.0.1

Clone the repository and install it:

(nrm)$ git clone https://github.com/BlueBrain/NeuroM.git
(nrm)$ pip install -e ./NeuroM

This 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.

• 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 = nrn.get_segment_lengths(ezy.TreeType.apical_dendrite)
>>> axon_sec_lengths = nrn.get_section_lengths(ezy.TreeType.axon)

• Visualize a neuronal morphology:

>>> # Initialize nrn as above
>>> fig, ax = ezy.view(nrn)
>>> fig.show()