SpikeInterface-Training-Milan-Sept25

Material for SpikeInterface Tutorial @ Human Technopole - Milan - September 2025

Schedule

Day 3 - Session 1 (2h) - Wed 24/09 14:00-15:00

1. 30min: Introduction to Spike Sorting (detailed theoretical) - Sam
2. 25min: Introductionto to SpikeInterface - Alessio
3. 5min: Installation check, get jupyter lab ready to go (trivial test notebook to run) - Chris

Day 3 - Session 2 (3h) - Wed 24/09 15:00-18:00

Step-by-step hands-on tutorial

1. Reading + Manipulation (30 min - Chris) Read data + visualize + select_channels+time_slice (DEMO + HAND-ON) Attach probe (on 32ch simulated recording): create a 4-shank probe with 8 channels and attach it to the simulated recording (DEMO) Save to JSON

2. Preprocess (DEMO - point to docs - skip remove artifacts + save recording - job_kwargs) (45 min) (Alessio) HAND-ON: apply+visualize preprocessing HAND-ON: check if there are bad channels and see if detect bad channels finds them all? (DEMO) Drift: only estimation + plotting for quality control (Sam)

3. Spike sort (DEMO - Kilosort4 - maybe ok on CPU) (30 min) (Sam) HAND-ON: run tridesclous2 - are there differences? #units / #spikes (optional: comparison) Comparison - plot agreements (DEMO)

4. Analyze Sorting (DEMO + HAND-ON) (45 min) (Chris) Create analyzer and compute extensions (DEMO) Hands-on 1: get the SNR distribution and plot an histogram Hands-on 2: plot ACG of best/worst SNR unit Hands-on 3: use the SI API to get extremum channels/amplitudes etc and plot the template in matplotlib

5. Curate (30 min) (Alessio) Threshold-based Model-based merge (Manual: SIGUI - teaser for next day)

Day 4 - Session 3 (3.5h) - Thu 25/09 09:30-13:00

1. 1hr: SpikeInterface-GUI - (DEMO + HANDS ON) (Sam)

2. 2.5hr: DEVELOP A FULL PIPELINE SCRIPT (Chris)

Installation

Please visit this page to install on your laptop python+spikeinterface.

Computing node with preinstalled environement will be also provided.

Dataset

Please download theses datasets on your laptop:

1. 4-tetrodes recording : ...
2. Nueopixels2.0 one-shank 20min : ...
3. In vitro recording : ...