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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