Tutorial¶
The NeuroM tutorial notebook¶
NeuroM includes tutorial notebooks under the tutorial
subdirectory
of the repository. You can launch the tutorials using MyBinder or with
Jupyter notebooks. Refer to Installation for help installing.
MyBinder¶
To launch the tutorial in your browser using MyBinder, click the 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.
morph_check: check the validity of a morphology file¶
The application morph_check allows you to apply semantic checks to a morphology file before loading it into NeuroM:
(nrm)$ morph_check -h # 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)$ morph_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)$ morph_stats -h # shows help for the morphometrics extraction script
(nrm)$ morph_stats path/to/files/filename # analyze single morphology file
(nrm)$ morph_stats path/to/files # analyze many morphology files