CtrlK
BlogDocsLog inGet started
Tessl Logo
SkillPublic

neuropixels-analysis

Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.

70

Quality

88%

Does it follow best practices?

Run evals on this skill

Adds up to 20 points to the overall score

View guide
SecuritybySnyk

Passed

No findings from the security scan

SKILL.md
Quality
Evals
Security

Quality

Content

82%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 highly actionable, well-sequenced pipeline guide whose code examples are executable end-to-end and whose detail is appropriately pushed into real one-level-deep reference files. The main weaknesses are mild redundancy (duplicated section/listing content) and missing validation checkpoints after the sorting and export stages.

Suggestions

Merge the 'Bundled Resources' section and 'Detailed Reference Guides' table into a single reference listing, and trim 'Overview'/'When to Use This Skill' to avoid restating the frontmatter description — this would tighten conciseness without losing information.

Add explicit validation checkpoints after risky or long-running stages: e.g., verify the preprocessed channel count after bad-channel removal, confirm the sorter output folder was created before postprocessing, and check that the exported .nwb file loads before declaring the pipeline done.

Document the bundled scripts 'explore_recording.py' and 'neuropixels_pipeline.py' (currently listed in scripts/ but never referenced in SKILL.md), or remove them from the bundle.

DimensionReasoningScore

Conciseness

The body is dense with pipeline-specific executable code and never explains concepts Claude already knows (no 'what is spike sorting' padding). However, 'Overview' and 'When to Use This Skill' largely restate the frontmatter description, and 'Bundled Resources' plus 'Detailed Reference Guides' list the same reference files twice — minor trimming that keeps it at anchor 4 rather than 5.

4 / 5

Actionability

Nearly everything is copy-paste-ready: 'si.read_spikeglx(\'/path/to/data\', stream_id=\'imec0.ap\')', the full preprocessing chain with parameters, 'si.run_sorter(\'kilosort4\', rec, folder=\'ks4_output\')' plus CPU alternatives, all 'analyzer.compute(...)' extensions with arguments, a thresholded curation query, and CLI invocations for every bundled script. Specific examples cover the common cases end-to-end, matching anchor 5.

5 / 5

Workflow Clarity

The 8-step 'Standard Analysis Workflow' is clearly sequenced and includes an explicit checkpoint — step 2 says 'Always check drift before spike sorting' with a '> 10' micron threshold gating whether correction is applied. It stops short of anchor 5 because later stages lack verification (no check that sorting output exists, no validation that the NWB export loads) and there are no feedback loops for error recovery.

4 / 5

Progressive Disclosure

All 10 referenced reference files exist and reference only external URLs (one level deep), scripts and the asset template are documented with CLI usage, and the SKILL.md works as an overview with quick-start inline. Minor organization gaps hold it at anchor 4: the reference files are listed twice (Bundled Resources section and Detailed Reference Guides table), and bundled scripts 'explore_recording.py' and 'neuropixels_pipeline.py' are never mentioned.

4 / 5

Total

17

/

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.

A strong description that clearly states what the skill does and when to use it, with concrete pipeline actions and specific trigger terms. The only weakness is keyword coverage that omits a few natural variations like 'ephys' and the raw file extensions.

DimensionReasoningScore

Specificity

The description lists multiple concrete, tool-named actions spanning the full pipeline — 'Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis' — which matches the anchor-5 example's comprehensive multi-action coverage. It is not a 4 because coverage runs end-to-end (ingest through curation) with specific named tools rather than leaving minor gaps.

5 / 5

Completeness

It explicitly answers both questions with concrete trigger phrases: the 'what' is the action list ('Load SpikeGLX/OpenEphys data... AI-assisted visual analysis') and the 'when' is the clause 'Use when working with neural recordings... or when the user mentions Neuropixels...'. This mirrors the anchor-5 example structure almost exactly, so a 4 ('when could be more explicit') does not fit.

5 / 5

Trigger Term Quality

The 'when' clause covers good natural keywords: 'neural recordings, spike sorting, extracellular electrophysiology, Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation'. It falls short of anchor 5 because common variations users actually say are missing — 'ephys', file extensions (.ap.bin, .meta, .nwb), and 'drift'/'spike sorted data' — while exceeding anchor 3's 'missing common variations' by including both tool names and workflow terms.

4 / 5

Distinctiveness Conflict Risk

Highly specific niche triggers — 'Neuropixels', 'SpikeGLX', 'Open Ephys', 'Kilosort', 'unit curation' — are unlikely to appear when another skill is needed, giving a clear niche with minimal conflict risk per anchor 5. It is written in third person, so no voice penalty applies.

5 / 5

Total

19

/

20

Passed

Validation

87%

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

Validation — 14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

14

/

16

Passed

Repository

synthetic-sciences/openscience

Path

backend/cli/skills/biology/neuropixels-analysis/SKILL.md

Reviewed

Table of Contents

Is this your skill?

If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.