SpikeInterface Training Bordeaux November 2025

Material for the SpikeInterface Tutorial organized in Bordeaux during the GDR NeuralNet by Pierre Yger and Samuel Garcia

Schedule

Tuesday 25/11

Morning session (9h00 - 12h00)

• Introduction to Spike Sorting (1h30) [P. Yger]

• Introduction to SpikeInterface (30 min) [S. Garcia]

• Check you install / downloads (15 min) [both]

• Tutorial 1 Reading + Manipulation (30 min) [S. Garcia]

  • Read and visualise data
  • The importance of probes

Afternoon session (13h00 - 17h00)

• Tutorial 2 Preprocessing (45 min) [P. Yger]

  • Apply and visualize preprocessing
  • Detect bad channels
  • Motion correction

• Tutorial 3 Spike sort (45 min) [S. Garcia]

  • Run a spike sorter
  • Compare spike sorter outputs

• Tutorial 4 Analyze Sorting (45 min) [P. Yger]

  • Create a SortingAnalyzer to explore your sorting
  • Compute some extensions
  • Play with the extension outputs

• Tutorial 5 Manual curation with Spikeinterface GUI (45 min) [S. Garcia]

  • Demo

• Tutorial 6 Automatic curation (45 min) [P. Yger]

  • Simple, threshold-based curation
  • Curation using ML models
  • Merging units

Wednesday 26/11

Morning session (9h00 - 12h00)

• Spike sorting on your own and/or other dataset [both]
  • bring your own data if any
  • Learn to spike sort all by yourself

Installation

See installation page

Overview of available datasets

If you have to pick only one file to download, because of disk usage, it has to be the first one, M25_D23_2024-11-11_13-11-10_OF1, since it will be the most used during the Tutorials. The download link is https://filesender.renater.fr/?s=download&token=f94a08b3-e779-4911-90bf-a312c3c34a01 Please do think about unzipping the data prior to the school!

In vivo

M25_D23_2024-11-11_13-11-10_OF1

Neuropixels 2.0 dataset (384 channels) acquired with the Open Ephys GUI in binary format. You can use the spikeinterface.extractor.read_openephys() function to read the data.

1544_2023-04-21_09-55-34_of

Recording with 16 channels organized in 4 tetrodes acquired with the Open Ephys GUI in "openephys" format. You can use the spikeinterface.extractor.read_openephys() function to read the data.

In vitro

mouse_CTX_14D.brw

Primary mouse cortex for E18 embryos. Plated 80K on CorePlate 1W38/60 3Brain, recorded after 14 days in culture with 3Brain BioCAM system. You can use the spikeinterface.extractor.read_biocam() function to read the data.

human_ngn2_100K_c_55D.brw

Human glutamatergic neurons induced via ngn2 method. Plated 100k on CorePlate 1W38/60 3Brain, recorded after 55 days in culture with 3Brain BioCAM system. You can use the spikeinterface.extractor.read_biocam() function to read the data.

Important

The 3Brain BioCAM system saves the data in unsigned integers. You should convert it to signed integers for a smooth processing. See documentation here. Note that the bit_depth for this system is 12!

Please download these datasets on your laptop from this link:

https://filesender.renater.fr/?s=download&token=f94a08b3-e779-4911-90bf-a312c3c34a01