Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add dralkh/seerai --skill neuropixels-analysisgit clone --depth 1 https://github.com/dralkh/seeraiWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/dralkh/seerai/neuropixels-analysis)<a href="https://agentmods.dev/skills/dralkh/seerai/neuropixels-analysis"><img src="https://agentmods.dev/badge/skills/dralkh/seerai/neuropixels-analysis/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/dralkh/seerai/neuropixels-analysis"><img src="https://agentmods.dev/badge/skills/dralkh/seerai/neuropixels-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00098 | $0.04088 |
| Opus 5.5 | $0.00039 | $0.01635 |
| Sonnet 5.5 | $0.00020 | $0.00818 |
| Haiku 4.5 | $0.00010 | $0.00409 |
Grade A, and why
neuropixels-analysis scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
91% identical to neuropixels-analysis — 147 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 406 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Neuropixels Data Analysis
Overview
Toolkit for analyzing Neuropixels high-density neural recordings using current best practices from SpikeInterface, the Allen Institute, and the International Brain Laboratory (IBL). It covers the full workflow from raw data to publication-ready curated units.
All examples use the real SpikeInterface API (spikeinterface.full as si) plus the
companion curation module (spikeinterface.curation as sc). The skill ships runnable
scripts in scripts/ and a copy-and-edit template in assets/ that implement this
workflow directly on top of SpikeInterface — there is no separate package to install
beyond the dependencies listed under Installation.
When to Use This Skill
This skill should be used when:
- Working with Neuropixels recordings (
.ap.bin,.lf.bin,.metafiles) - Loading data from SpikeGLX, Open Ephys, or NWB formats
- Preprocessing neural recordings (filtering, common reference, bad-channel detection)
- Detecting and correcting motion/drift
- Running spike sorting (Kilosort4, SpykingCircus2, Mountainsort5, Tridesclous2)
- Computing quality metrics (SNR, ISI violations, presence ratio, amplitude cutoff)
- Curating units (threshold-based, model-based, or AI-assisted)
- Creating visualizations and exporting to Phy or NWB
Supported Hardware & Formats
| Probe | Electrodes | Channels | Notes |
|---|---|---|---|
| Neuropixels 1.0 | 960 | 384 | Use phase_shift for ADC correction |
| Neuropixels 2.0 (single) | 1280 | 384 | Denser geometry |
| Neuropixels 2.0 (4-shank) | 5120 | 384 | Multi-region recording |
| Format | Extension | Reader |
|---|---|---|
| SpikeGLX | .ap.bin, .lf.bin, .meta |
si.read_spikeglx() |
| Open Ephys | .continuous, .oebin |
si.read_openephys() |
| NWB | .nwb |
si.read_nwb() |
Quick Start
Import and configure parallel processing
import spikeinterface.full as si
# Global job kwargs are reused by all parallelizable steps
si.set_global_job_kwargs(n_jobs=-1, chunk_duration="1s", progress_bar=True)
What ships with it
17 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- assets/analysis_template.py 8.8 KB runs code
- references/AI_CURATION.md 5.7 KB
- references/ANALYSIS.md 9.6 KB
- references/api_reference.md 7.2 KB
- references/AUTOMATED_CURATION.md 13 KB
- references/MOTION_CORRECTION.md 8.4 KB
- references/plotting_guide.md 11 KB
- references/PREPROCESSING.md 6.5 KB
- references/QUALITY_METRICS.md 9.2 KB
- references/SPIKE_SORTING.md 7.6 KB
- references/standard_workflow.md 9.2 KB
- scripts/compute_metrics.py 5.1 KB runs code
- scripts/explore_recording.py 5.4 KB runs code
- scripts/export_to_phy.py 2.4 KB runs code
- scripts/neuropixels_pipeline.py 13 KB runs code
- scripts/preprocess_recording.py 4.2 KB runs code
- scripts/run_sorting.py 2.5 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago First seen · 406 lines · 98 tokens per session scan A 0e322c9584d4
neuropixels-analysis is a skill published in the GitHub repository dralkh/seerai (94 stars, last pushed 20d ago), licensed MIT. It adds 98 tokens to every session and 4,088 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 91% identical to neuropixels-analysis, differing in 147 lines, and is treated as a copy.
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