Versioned security assessment

Report ID: SA-581AC30B

6/30/2026, 5:27:22 AM

neuropixels-analysis security assessment v5

Skill Security Certification Report

Audit History
Audit model: codex Historical report
Skill name
neuropixels-analysis
Version
v5
Maintainer
K-Dense-AI
Source
github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/neuropixels-analysis
Coverage
18 Files scanned · 5,358 Lines analyzed
Policy version
Unavailable

Highest confirmed finding severity

Medium

3 confirmed security findings require attention.

Installation context

Historical evidence

This report may not describe the currently installable artifact. Open the current Skill page for install guidance.

Open current Skill page

This report does not block or authorize the manifest or ZIP.

Static analysis reported many high-risk patterns, but review found most command, weak-crypto, C2, and reconnaissance hits are false positives from Markdown examples or neuroscience terminology. The confirmed risks are legitimate for this skill: executable Python scripts write local analysis outputs, SpikeInterface may run external spike sorters, and optional AI-assisted curation can send generated unit plots to third-party API clients. No prompt injection attempts, malicious credential exfiltration, or hidden network callbacks were found.

Report position

Historical report

Open audit history before using this report to install.

Audit attestation

Not attestable

The required immutable binding is incomplete.

Human verification

Not verified

No human verification is recorded for this report.

Coverage

18 Files scanned · 5,358 Lines analyzed

3 items shown for review

Limitations

This report does not claim runtime or sandbox execution and does not prove the absence of side effects.

Evidence chain

Follow the evidence from source binding to the install contract. Available evidence supports verification; it is not a safety guarantee.

  1. Source

    Binding unavailable

  2. Artifact

    Identity incomplete

  3. Audit

    Complete

  4. Install contract

    Open manifest to verify

    Open manifest

Capabilities observed

Observed means this report recorded supporting evidence. Not recorded does not prove that a capability is absent.

Contains scripts

May execute code included with the Skill.

Observed in 4 evidence locations

Network access

May connect to external services.

Observed in 3 evidence locations

Filesystem access

May read or write local files.

Observed in 6 evidence locations

Env variables

May read values from the process environment.

Not recorded by this audit

External commands

May invoke commands or programs outside the Skill.

Observed in 5 evidence locations

Risk findings

Confirmed security concerns are separated from items that still need review.

Confirmed security concerns (3)

RISK-001 Medium
scripts/run_sorting.py:59-66scripts/neuropixels_pipeline.py:174-189assets/analysis_template.py:142-149
External Spike Sorter Execution Through SpikeInterface
The scripts invoke SpikeInterface run_sorter with a selected sorter such as Kilosort4, Kilosort3, SpykingCircus2, or Mountainsort5. This is expected scientific workflow behavior, but it can execute installed sorter toolchains or containerized dependencies on local Neuropixels data.
Direct calls to si.run_sorter are present in executable scripts and templates. The sorter choices are constrained and domain-appropriate, so this is a legitimate elevated-risk capability rather than malicious command injection.
RISK-002 Medium
scripts/preprocess_recording.py:72-83scripts/compute_metrics.py:57-67scripts/compute_metrics.py:98-135scripts/neuropixels_pipeline.py:326-343assets/analysis_template.py:235-237
Local Filesystem Writes To User-Selected Output Paths
The bundled scripts create output directories and write preprocessed recordings, quality metrics, labels, summaries, plots, analyzer folders, and Phy exports. This is required for analysis, but users should run it in intended project directories because large files can be created or overwritten.
The code explicitly creates folders and writes CSV, JSON, binary-folder analyzer data, plots, and export directories. These writes are bounded by user-provided output paths and do not target sensitive system locations.
RISK-003 Medium
references/AI_CURATION.md:57-72references/AI_CURATION.md:284-313SKILL.md:140-153
Optional Third-Party AI Curation May Share Scientific Data
The AI-assisted curation guide shows Anthropic and OpenAI client usage for visual unit analysis. This is optional and user-configured, but generated plots or unit summaries may leave the local environment when an API client is used.
The references document API clients and visual curation workflows, but no bundled script silently sends data by default. The privacy risk depends on whether the user enables an external API client.

Expert evidence

Immutable subject identity, scanner metadata, dismissed matches, and source-level evidence.

Artifact subject

Marketplace commit
Unavailable
Content hash
Unavailable
Tree hash
Unavailable
Skill path
Unavailable
Audit payload hash
Unavailable

Analysis metadata

Audit model: codex

Analysis state: Complete

Scope is limited to the recorded files, lines, methods, and evidence. No runtime or sandbox execution is claimed.

Static false positives ignored (4)
Low
SKILL.md:241-263SKILL.md:297-316references/AUTOMATED_CURATION.md:35-43references/SPIKE_SORTING.md:18-21
Markdown Command Examples Misclassified As Backtick Execution
Many external command detections are fenced Bash or Python examples in documentation, such as resource usage, install commands, and user-invoked scripts. They are not Ruby backtick execution and do not run automatically when the skill is loaded.
The flagged locations are clearly inside Markdown code fences or documentation examples. They describe commands users may run manually rather than executable code paths in the skill runtime.
Low
assets/analysis_template.py:169-176references/SPIKE_SORTING.md:143-168references/plotting_guide.md:268-282references/ANALYSIS.md:23-37
Weak-Crypto And C2 Keyword Hits Are Neuroscience False Positives
The weak cryptography and C2 detections map to domain words and symbols such as spike amplitudes, SC2 sorter names, MUA labels, thresholds, and metric abbreviations. No hashing, encryption, beaconing, or command-and-control behavior was found in the reviewed contexts.
Reviewed examples are scientific analysis terms and plotting code. They do not perform cryptographic operations or network control behavior.
Low
references/AI_CURATION.md:296-308
API Key Examples Use Placeholders Rather Than Embedded Secrets
The env_access findings point to documentation examples that use placeholder strings for API keys. No real secret value or process environment extraction was found at those locations.
The reviewed lines show api_key="your-api-key" in documentation. This is a placeholder pattern, not a hardcoded credential or credential harvesting behavior.
Low
scripts/explore_recording.py:21-33scripts/preprocess_recording.py:29-45scripts/neuropixels_pipeline.py:39-42references/SPIKE_SORTING.md:334-339
System Reconnaissance Hits Are Local Recording Metadata Prints
The reconnaissance detections correspond to printing recording dimensions, durations, sampling rates, GPU availability examples, and local progress information. This is expected data exploration output for electrophysiology workflows.
The reviewed code reports properties of the loaded recording or local compute environment for analysis setup. No host inventory, credential discovery, or network reconnaissance was found.

Verify and export

JSON report CITATION.cff SARIF 2.1.0 Signed installation manifest

The manifest and lockfile bind install artifacts to cryptographic hashes. This integrity claim is separate from the security assessment.

Audit attestation: not_attestable