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neuropixels-analysis

Analyzes 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.

68

Quality

86%

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

75%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A strong, highly actionable body: fully executable code for every pipeline stage, a clearly sequenced workflow with real validation checkpoints, and a well-verified one-level reference structure. The main weakness is token efficiency — scattered version/date pins and redundant script documentation could be consolidated or pushed to references.

Suggestions

Consolidate version- and date-sensitive notes (SpikeInterface 0.105.0 behaviors, the read_phy bug, zarr pin, Python 3.13 test env) into a single 'Version compatibility' or 'Known issues' section instead of scattering them across workflow steps.

Trim the 'Bundled Resources' section: the per-script one-liners duplicate the Quick Start pipeline call and the inline references to each script elsewhere; a compact table of script → purpose with pointers to the reference guides would save substantial tokens.

Move 'Key Parameters to Adjust' and 'Project Structure' into the existing references (e.g. standard_workflow.md or api_reference.md) and link to them, keeping SKILL.md a leaner overview of the workflow.

DimensionReasoningScore

Conciseness

The body is operational with no conceptual over-explanation, but version/date pins are scattered across many sections ('Targets SpikeInterface 0.105.0... (reviewed 2026-10-01)', 'These flags match SpikeInterface 0.105.0', 'SpikeInterface 0.105.0 has no export_to_nwb', 'zarr>=2.18,<3', Python 3.13) rather than consolidated, and 'Bundled Resources' re-documents scripts already shown in Quick Start. This fits 'mostly efficient but could be tightened' rather than 'minor instances', especially given the rubric's explicit penalty for scattered time-sensitive information.

3 / 5

Actionability

Every workflow step ships complete, executable code with real API calls and arguments (read_spikeglx with stream_name, run_sorter with do_correction=False, a concrete pandas curation query, export commands), plus runnable bash commands for all bundled scripts and specific parameter ranges. Code is copy-paste ready and covers the common cases (SpikeGLX/Open Ephys/NWB, multiple sorters).

5 / 5

Workflow Clarity

A clear numbered 1–8 sequence (preprocess → drift → sort → postprocess → curate → export) with genuine validation checkpoints ('Validate AP stream, calibration, channel order, probe geometry and segment boundaries first', 'Always inspect drift before sorting', 'validate the resulting NWB file', inspect model requirements before loading). It stops short of the top anchor because explicit error-recovery feedback loops (validate → fix → retry) are not spelled out.

4 / 5

Progressive Disclosure

Good structure: the core workflow is inline, and all ten detailed guides live in references/ (verified to exist, one level deep, clearly presented in a table plus in-context links), with scripts and a template bundled. However, the ~450-line body also carries the full workflow, key parameters, pitfalls, project structure, and a citation block — heavier than a lean overview with some content that belongs in references, matching 'good structure with minor organization gaps'.

4 / 5

Total

16

/

20

Passed

Description

92%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

An excellent description: concrete, comprehensive, third-person, with an explicit 'Use when' trigger clause. The only gap is missing file extensions and a few common synonyms in the trigger terms.

Suggestions

Add the file extensions users naturally mention to the trigger clause, e.g. 'Use when working with Neuropixels 1.0/2.0 recordings (.ap.bin/.lf.bin/.meta, .continuous, .nwb), spike sorting, or ephys analysis.'

DimensionReasoningScore

Specificity

The description enumerates multiple concrete actions covering the full pipeline — '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)' — with named tools and sub-methods, matching the comprehensive-coverage anchor. Third-person voice ('Analyzes', 'Covers') is used throughout, so no voice penalty applies.

5 / 5

Completeness

Both questions are explicitly answered: a clear 'what' (the full end-to-end pipeline enumeration) and a concrete 'when' ('Use when working with Neuropixels 1.0/2.0 recordings, spike sorting, or extracellular electrophysiology analysis'), matching the top anchor exactly.

5 / 5

Trigger Term Quality

Good natural keyword coverage — 'Neuropixels 1.0/2.0 recordings', 'spike sorting', 'SpikeGLX', 'Open Ephys', 'NWB', 'extracellular electrophysiology' — but file extensions users would mention (.ap.bin, .lf.bin, .meta) and the common synonym 'ephys' are absent, so it falls short of the comprehensive-synonyms-and-extensions anchor.

4 / 5

Distinctiveness Conflict Risk

The Neuropixels/SpikeInterface niche is unambiguous and its triggers would not naturally fire for unrelated skills; overlap risk with a generic electrophysiology or NWB skill is minimal, matching the clear-niche anchor.

5 / 5

Total

19

/

20

Passed

Validation

93%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_field

'metadata' should map string keys to string values

Warning

Total

15

/

16

Passed

Repository

K-Dense-AI/scientific-agent-skills

Path

skills/neuropixels-analysis/SKILL.md

Reviewed

Table of Contents

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