neuropixels-analysis
Category: life-sciences · License: MIT · Version: 2.4 · Includes scripts
Tags: Neuropixels, spike sorting, electrophysiology, SpikeInterface, neuroscience
When to use it
Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, quality metrics, and unit curation (threshold-based, model-based UnitRefine, and AI-assisted visual review). Use when working with Neuropixels 1.0/2.0 recordings, spike sorting, or extracellular electrophysiology analysis.Example requests
Ask your agent in plain language, for example:- “How do I get my Neuropixels 2.0 data sorted with Kilosort4 through SpikeInterface?”
- “I recorded from mouse V1 with a Neuropixels 1.0 probe using SpikeGLX. The folder is session01_g0/ with session01_g0_t0.imec0.ap.bin and the .meta file. I loaded it with si.read_spikeglx but the traces look noisy and the sorted units look split across depth, with the probe drifting a lot over the 90 min recording. What should I do before re-running Kilosort4?”
- “I have a sorted dataset with a few hundred units from a high-density silicon probe in mouse cortex. Many look like noise or multi-unit activity. How can I automatically decide which are good single neurons, and look at the borderline ones, without writing every rule myself?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.