Material for spike sorting school for WIRED 2024 meeting.
Spikeinterface session, 2024 March 13th
Here in this repository:
-
some python script:
- convert_data.py : convert neuralynx framgented into binary format
- visualize_raw_data.py: simple viewer for traces
-
some notebook:
- demo_simulated_dataset.ipynb
- adtech_sub-001.ipynb
- adtech_sub-002.ipynb
- dixi_sub-003.ipynb
- dixi_sub-004.ipynb
- Overview spike sorting - 40 min (Pierre)
- Overview spikeinterface - 20 min (Sam)
- Demo notebook with simulated dataset - 20 min (Sam)
- Demo notebook with simulated dataset drifting - 10 min (Sam)
- Hands-on on the same notebook - 30 min (all participants)
- Tutorial on noise measurement - 5 min (Sam)
- Demo real data - 30 min (Pierre)
- Hands-on real data - 30 min (all participants)
- Bonus time : exaplore your own dataset if you want to stay one hour more.
Procedure for Windows/Apple:
If you already have anaconda/vscode installed jump to 4.
- Step 1 : If your username/login has spaces and/or weird symbols, YOU MUST create a new user with a simpler name (no spaces, no symbols). Login with such a user name.
- Step 2: download anaconda from here https://www.anaconda.com/download For Windows users (even though it is sometimes not recommended) we advise to check “Anaconda to your path”. It will help with vscode compatibility.
- Step 3 : If you do not have a code editor we advise installing vscode. https://code.visualstudio.com/download. After installation, you can add the plugins “python” and “jupyter”
- Step 4 : Go to this page https://github.com/samuelgarcia/school_spike_sorting_WIRED_2024
- Step 5 : click on "code" (green button) and download the zip. Etxract the zip.
- Step 6 : Open the anaconda prompt (a terminal).
- Step 7 : go at the correct place where the zip is etracted.
This command is a tip not the good one :
cd C:/users/myusername/where_the_zip_is
- Step 8 : create the python environement
conda env create -f spikeinterface_environment.yml
. This can take a while and download many paquets. This need bandwith. Do not expect to do this during the tutorial
Procedure for linux ubuntu/debian style:
anaconda on linux is sometimes messing a lot for new users. Standard installation using system and pip are faster and easier to manage.
sudo apt install python3.11 python3.11-venv python3.11-dev
mkdir ~/.virtualenvs
python3.11 -m venv ~/.virtualenvs/si_env
source ~/.virtualenvs/si_env/bin/activate
pip install --upgrade pip
pip install spikeinterface[full]
pip install PySide6
pip install jupyterlab
pip install https://github.com/NeuralEnsemble/python-neo/archive/master.zip
pip install https://github.com/SpikeInterface/spikeinterface/archive/main.zip
pip install https://github.com/SpikeInterface/spikeinterface-gui/archive/main.zip
pip install https://github.com/magland/sortingview/archive/main.zip
pip install https://github.com/NeuralEnsemble/ephyviewer/archive/master.zip
The dataset will be provide the workshop day by USB key.
Please copy the data on your drive during the training session and then remove the data for always.