neuropixels-analysis SKILL.md skillA
neuropixels-analysis from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/neuropixels-analysis@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/scientific-computing/neuropixels-analysis/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 14,810 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Pipeline for Neuropixels extracellular electrophysiology: probe geometry (ProbeInterface), Kilosort sorting via SpikeInterface, quality metrics, unit curation (ISI, firing rate, SNR), post-sort analysis (PSTH, tuning curves, population decoding). Supports Neuropixels 1.0/2.0/Ultra in rodent/primate experiments.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Neuropixels Analysis ## Overview Neuropixels probes record extracellular voltage from 384 (NP 1.0) or 192 (NP 2.0) simultaneously recorded channels at 30 kHz. Analysis follows a canonical pipeline: raw data → spike sorting (Kilosort) → quality curation → unit analysis. **SpikeInterface** (Python) provides a unified API across 10+ spike sorters, handles data loading from multiple formats (SpikeGLX, OpenEphys, NWB), computes quality metrics, and exports sorted results. **ProbeInterface** manages probe geometry and channel maps. Post-sort analysis (PSTHs, firing rate, decoding) uses standard Python scientific stack. ## When to Use - Spike-sorting Neuropixels recordings from SpikeGLX (`.bin`) or OpenEphys (`.dat`) to extract single-unit activity - Applying automatic quality control metrics (ISI violations, SNR, firing rate) to curate sorted units - Computing peristimulus time histograms (PSTHs) locked to experimental events - Analyzing population coding: decoding stimulus or behavioral variables from firing rates - Converting sorted data to NWB (Neurodata Without Borders) format for sharing - Comparing multiple spike sorters on the same dataset for method validation …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/neuropixels-analysis@sha256:b8c31b6801e3907cThe line at the top of this page pins the label git:20260428.81ea2d2, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_euppwnvjdzlwmybk)
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Versions
The registry has recorded 2 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 69 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 14,810 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 14,963 B | A | view |
Audit of the latest version
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- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (14810 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
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Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_euppwnvjdzlwmybk GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/neuropixels-analysis GET https://markdownregistry.com/api/v1/blob/b8c31b6801e3907cadf0ecb60d92664c0bea9ede101da6ff8744e4fec39d0e8e
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