This example shows how to run the MountainSort v4 spike sorting algorithm using a bash script. This does not include the automated curation and is just intended to illustrate MountainLab usage from the command-line and using simple bash scripts. The recommended way to run spike sorting is by using python scripts and/or JupyterLab. See the documentation for more details.
First you must install the latest version of mountainlab and at least the following mountainlab packages (see docs for installation instructions):
- ml_ephys
- ml_ms4alg
In order to view the result you can also install ephys-viz and optionally qt-mountainview (see docs for installation instructions).
Create a synthetic dataset by running:
./synthesize_dataset.sh
This will create some files in the dataset/ directory. To view the dataset (using ephys-viz):
ev-dataset dataset
Next, run the spike sorting:
./ms4_sort_bash.sh
This should create an output directory with some files, including a firings.mda file.
Now, view the results using any of the following:
ev-templates output/templates.mda.prv
ev-timeseries dataset/raw.mda.prv --firings output/firings.mda.prv --samplerate=30000
qt-mountainview --raw dataset/raw.mda.prv --filt output/filt.mda.prv --pre output/pre.mda.prv --samplerate 30000 --firings output/firings.mda