samuelgarcia / school_spike_sorting_wired_2024

Material for spike sorting school for WIRED 2024 meeting

school_spike_sorting_WIRED_2024

Material for spike sorting school for WIRED 2024 meeting.

https://wired-icm.org/

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

Approximative timeline : 3 hours + bonus

• 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.

Installation

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

Dataset

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.