Tutorial

The NeuroM tutorial notebook

NeuroM includes tutorial notebooks under the tutorial subdirectory of the repository. You can launch the tutorials using MyBinder, no need to download or install!

MyBinder

To launch the tutorial in your browser using MyBinder, click the badge badge

Jupyter notebooks

For a detailed explanation on installing and running Jupyter/IPython notebooks, we refer to the Jupyter/IPython Notebook Quick Start Guide.

First, install jupyter in the virtual environment. Second, launch the Jupyter Notebook App. Make sure that you launch the application from a folder that contains the NeuroM Tutorial notebook.

(nrm)$ pip install jupyter
(nrm)$ cd /path/to/dir/containing/notebook
(nrm)$ jupyter notebook                    # launch the Jupyter Notebook App

Next, you can select the notebook that you want to open. Now, you can go through the tutorial and learn about loading, viewing, and analyzing neuronal morphologies!

Applications using NeuroM

NeuroM ships with configurable command line applications for commonly needed functionality.

neurom check: check the validity of a morphology file

The application neurom check allows you to apply semantic checks to a morphology file before loading it into NeuroM:

(nrm)$ neurom check --help                  # shows help for morphology checking script

Try it yourself! You can go to NeuroMorpho.Org to download a neuronal morphology and perform the semantic checks:

(nrm)$ neurom check path/to/files/filename

morph_stats: extract basic morphometrics of a sample morphology

The application morph_stats extracts various morphometrics for one or many morphologies. Its contents can be easily configured via a configuration file, as shown in the online documentation.

(nrm)$ neurom stats --help                  # shows help for the morphometrics extraction script
(nrm)$ neurom stats path/to/files/filename  # analyze single morphology file
(nrm)$ neurom stats path/to/files           # analyze many morphology files