nolanlab_ephys

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

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

Then you can run anything you'd like using uv e.g.

uv run code .

or make a venv using

uv venv

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/chrishalcrow/nolanlab-ephys.git
cd nolanlab-ephys

Now you can run some scripts! Each script is kept in scripts/experiment/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

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