SpikeInterface-Training-Edinburgh-May24

Material for the SpikeInterface training day, part of the Tools and Methods for Next Generation Electrophysiology Workshop.

Taking place on Tuesday May 28th at the University of Edinburgh in the Informatics Forum, room G.07.

To do before the training:

1. Install SpikeInterface, using the installation guide below
2. Download the dataset for the tutorials
3. Run the pre_workshop_tests notebook to make sure your installion is working properly

If you have any problems, find an expert on Monday.

Schedule

Time	Topic	Presenter(s)	Type
Morning	Overview and Tutorials (3.5 hours)
9:00 - 10:00	Spike sorting overview	Pierre	Talk
10:00 - 10:45	Spikeinterface overview	Alessio	Talk
	break
11:00 - 11:20	Ultra quick demo (simulated)	Sam	Demo
11:20 - 12:30	Long demo (Cambridge Neurotech data)	Sam	Demo
Afternoon	Guided Hands-on (4 hours)
14:00 - 14:15	Object interaction cookbook	Heberto	Talk
14:15 - 14:30	Probe handling	Zach	Hands-on
14:30 - 14:50	Preprocessing	Alessio	Talk
14:50 - 15:10	Drift with generated data	Pierre	Talk
15:10 - 15:30	Postprocessing	Chris	Hands-on
	break (20 min)
15:50 - 16:10	Visualization (Sortingview, Sigui)	Alessio, Sam	Hands-on
16:10 - 16:30	Metrics & Curation (Automerge, etc.)	Aurelien	Hands-on
16:30 - 16:40	Benchmark (simulated)	Sam	Talk
16:50 - 17:10	Export to NWB (neuroconv)	Heberto	Hands-on
	break (20 min)
Bonus Track
17:30 - 18:30	Hands-on with your own dataset		Hands-on

Installation

Procedure for Windows/Apple:

If you already have anaconda/vscode installed jump to Step 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/SpikeInterface/SpikeInteface-Training-Edinburgh-May24
• 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 wait to do this during the tutorial, it can be time consuming

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_tutorial
• source ~/.virtualenvs/si_tutorial/bin/activate
• pip install --upgrade pip
• pip install spikeinterface[full,extractors]
• pip install PySide6
• pip install jupyterlab
• pip install sortingview
• 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/NeuralEnsemble/ephyviewer/archive/master.zip
• pip install neuroconv
• pip install dandi
• pip install remfile

Dataset

Please download datasets from this link and unzip them:

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