spikelab

name	spikelab
description	Sets up and manages the SpikeLab environment. Clones the repository, installs the library, generates repo maps, and delegates to in-repo skills for analysis, spike sorting, development, and education. Use when the user wants to work with SpikeLab.

SpikeLab

SpikeLab is a Python library for loading, analyzing, visualizing, and exporting neuronal spike train data from multi-electrode array (MEA) electrophysiology experiments.

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Session Start — Environment Detection

Run this detection sequence once at the start of every session:

1. Check if spikelab is importable in the default python:

   python -c "import spikelab; print('OK')" 2>/dev/null
   

   If this succeeds, use bare python for all commands.

2. If it fails, check for a spikelab conda environment:

   conda env list 2>/dev/null | grep spikelab
   

   If found, prefix all commands with conda run -n spikelab for the rest of the session.

3. If neither works, read INSTALL.md in this skill directory for full installation instructions. Prefer the conda approach (Option A) unless the user specifies otherwise.

Use the detected invocation method consistently for all Python/pip commands in the session.

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Delegation

Once SpikeLab is available, delegate to the appropriate in-repo skill based on the user's request:

Spike sorting — the user wants to sort raw recordings, configure sorting parameters, curate units, assess sorting quality, or troubleshoot sorting failures:

SpikeLab/src/spikelab/agent/skills/spikelab-spikesorter/SKILL.md

It covers: sort_recording, sort_multistream, curation, QC figures, and loading/inspecting sorted results. Outputs are saved as sorted_spikedata_curated.pkl files that the analysis implementer can load.

Explanatory and conceptual questions — the user asks what an analysis does, how a method works, what a result means, wants to understand the underlying neuroscience, or asks about SpikeLab's API and data structures:

SpikeLab/src/spikelab/agent/skills/spikelab-educator/SKILL.md

It contains concept definitions, interpretation guidance, literature references, and cross-references to documentation, examples, and source code.

Library development — the user wants to integrate analysis code into the library, promote a script's computations to reusable methods, add new functionality, write tests, or expose methods through MCP:

SpikeLab/src/spikelab/agent/skills/spikelab-developer/SKILL.md

It covers the full integration pipeline: auditing scripts against existing methods, replacing reimplementations, adding novel methods, writing tests (main usage + edge cases), MCP exposure, and PR submission.

Data analysis and visualization — loading sorted data, running analyses, producing figures, writing scripts, and any ambiguous requests that are not sorting-related or development-related:

SpikeLab/src/spikelab/agent/skills/spikelab-analysis-implementer/SKILL.md

It contains the full analysis workflow: API orientation via repo maps, script structure, workspace usage, figure conventions, and reporting. It knows how to load sorting outputs from sorted_spikedata_curated.pkl files.

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Repo Maps

The repo maps do not ship with the repository — they must be generated after installation and after every library update. Without them, the analysis-implementer, educator, developer, and spike-sorter skills cannot orient themselves to the library API and will produce unreliable results.

Run the spikelab-map-updater skill to generate REPO_MAP.md and REPO_MAP_DETAILED.md:

SpikeLab/src/spikelab/agent/skills/spikelab-map-updater/SKILL.md

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Quick Reference

What	Where
Library source	SpikeLab/src/spikelab/
Repo maps (API docs)	SpikeLab/src/spikelab/agent/skills/spikelab-map-updater/REPO_MAP.md, REPO_MAP_DETAILED.md
Map updater skill	SpikeLab/src/spikelab/agent/skills/spikelab-map-updater/SKILL.md
In-repo spike sorter skill	SpikeLab/src/spikelab/agent/skills/spikelab-spikesorter/SKILL.md
In-repo developer skill	SpikeLab/src/spikelab/agent/skills/spikelab-developer/SKILL.md
In-repo analysis skill	SpikeLab/src/spikelab/agent/skills/spikelab-analysis-implementer/SKILL.md
In-repo educator skill	SpikeLab/src/spikelab/agent/skills/spikelab-educator/SKILL.md
Installation guide	INSTALL.md (this skill directory)