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:

It will take in raw ephys recordings

data_folder/
    global_session_type/
        M{mouse:02d}_D{day:02d}_*_{session_type}/
            Record Node 109/         <---- (or whatever openephys spits out)

And output SortingAnalyzers with the naming convention:

deriv_folder/
    M{mouse:02d}/
        D{day:02d}/
            probe_layout.pdf
            {session_type}/
                {protocol}/
                    sub-{mouse:02d}_day-{day:02d}_ses-{session}_srt-{protocol}_analyzer

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

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

We recommend that you make a fork (your own personal copy) of this repo by clicking Fork -> Create new fork above. To begin using the fork on your computer, please download (clone) the repo from github. Then enter the directory and start using the codebase!

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

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

uv run scripts/template/sort_on_comp.py 25 25 VR kilosort4 --data_folder /path/to/data/folder --deriv_folder /path/to/deriv/folder

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.

You can visualise the results using e.g.

uv run scripts/template/visualise_results.py 25 25 VR kilosort4 --deriv_folder /path/to/deriv/folder

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/template/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