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