Spike sorting school - Cajal - Bordeaux 2024

Material for the spike sorting/SpikeInterface training day, part of the Cajal movement and motor control 2024.

To do before the training:

1. Install SpikeInterface, using the installation guide below
2. Download the dataset for the tutorials

Schedule

Tuesday 19th November

11:00-11:45 Introduction to spike sorting

11:45-12:300 Overview of SpikeInterface + demo

14:00 18:00 : SpikeInterface detailed handons and tutorials

• Object interaction cookbook 15min
• Probe handling 15min
• Preprocessing 20min
• Drift with generated data 20min
• Postprocessing 20min
• Visualization (Sortingview, Sigui) 20min
• Metrics & Curation (Automerge, etc.) 20min
• Sorting on your own dataset 30min

18:00 19:00 EMUsort Samuel Sober

Given the limited time, the hands-on session is more a follow-along guided tutorials. You can download all notebooks on this repo.

Installation

This procedure use the new uv fast installer for python.

Procedure for Windows/Apple/Linux:

1. On macOS and Linux. Open a terminal and do $ curl -LsSf https://astral.sh/uv/install.sh | sh
2. On windows. Open a powershell and do powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
3. exit session and log again.
4. Go to this page https://github.com/samuelgarcia/school_spike_sorting_neuralnet_saclay_2024
5. Click on "code" (green button) and download the zip. Etxract the zip.
6. open terminal or powershell
7. Go to the correct folder cd C:/users/myusername/where_the_zip_is
8. Create an empty env uv venv si_env --python 3.11
9. Activate the env source si_env/bin/activate (you should have (si_env) in your terminal)
10. uv pip install -r requirements_tutorial.txt

Do not wait to do this during the tutorial, it can be time consuming

For installtion, you can have more information here

Dataset

Please download datasets from this link and unzip them:

https://drive.google.com/drive/folders/17RlgsMLheW82IMLMgmTFifVACebDZ8X5?usp=sharing