nolanlab-ephys

This is the main repo for processing ephys data in the Nolan Lab. The pipeline step takes in raw ephys data and outputs a SpikeInterface sorting analyzer:

Read about the entire NolanLab pipeline: https://github.com/MattNolanLab/analysis_pipelines

You can visualise the output of this pipeline using: https://github.com/MattNolanLab/clusters

This repo represents a minimum viable product: it contains a working spike sorting pipeline. But it has been forked and modified when applied to other projects in the lab. The modified repos can be found here:

• https://github.com/chrishalcrow/nolanlab-ephys (Code which sorts Harry, Bri, Wolf, Junji and Teris' data can be found in scrips/{experimenter_name})

Use on your own computer

To begin using this repo, please download (clone) the repo from github. Then enter the directory and start using the codebase!

git clone https://github.com/MattNolanLab/nolanlab-ephys
cd nolanlab-ephys

Then you can run anything you'd like using (uv)[https://docs.astral.sh/uv/getting-started/installation/] e.g.

uv run scripts/template/sort_on_comp.py

Read more about the sort_on_comp.py script by opening the file: there's lots of documentation inside.

The different spike sorting protocols can be found in src/nolanlab_ephys/si_protocols.py.

Using on EDDIE

The package is designed to be used on the Nolan Lab's data on your local computer or on EDDIE, the Edinburgh supercomputer. To run a spike sorting pipeline on Eddie, do the following. First, log on to EDDIE and get a login node:

ssh edinburgh_username@eddie.ecdf.ed.ac.uk
... wait to get on to eddie ...
qlogin -l h_vmem=8G

We'll now install this package. EDDIE has a 2TB scratch you can use to put stuff in. We'll navigate to there (then into wherever you want to store this code. I've made a my_project/code folder), download ("clone") this package, then navigate into the package:

cd /exports/eddie/scratch/chalcrow/my_project/code
git clone https://github.com/MattNolanLab/nolanlab-ephys.git
cd nolanlab-ephys

Now you can run some scripts! Each script is kept in scripts/experimenter_name/blah.py. Each step of each experimenters pipeline bespoke script. For it to run, it needs to know some info. For spike sorting it needs to know the: mouse, day, sessions, sorting protocol, folder to put the data on the scratch, folder to put the derivatives on the scratch. Here's an example on my login (note: you need to change chalcrow to something else):

uv run scripts/wolf/sort_on_eddie.py 25 20 OF1,VR,OF2 kilosort4A --data_folder /exports/eddie/scratch/chalcrow/wolf/data/ --deriv_folder /exports/eddie/scratch/chalcrow/wolf/derivatives