Optogenetics Protocol Designer (Claude Skill)

Helps Claude specify an optogenetics experiment end to end — which opsin matches the manipulation you want, what light parameters its kinetics allow, where to place the fiber, and which controls make the result interpretable.

   
Type Claude Skill
Supplier Awesome Cognitive and Neuroscience Skills (community OSS, MIT)
Availability GA — one of ~40 research skills in the collection (last upstream push 2026-07-13)
Pricing Free / OSS (MIT)
Capabilities Read-only — experimental-design guidance; no software is executed
Verified works · 2026-08-06
Security cleared · 2026-08-06 — legitimate NeuroAIHub repo transfer confirmed, MIT, no credential requests

How to install

  • Claude Code — plugin marketplace (installs all skills in the collection): 
    /plugin marketplace add HaoxuanLiTHUAI/awesome_cognitive_and_neuroscience_skills
/plugin install awesome-cognitive-and-neuroscience-skills@awesome-cognitive-and-neuroscience-skills

    Restart Claude Code afterwards. The skills are description-activated — there is no slash command; describe the manipulation you want and Claude loads the skill.

  • Claude Code — single-skill alternative. This skill declares a required dependency on the collection’s research-literacy skill, so copy both: 
    git clone https://github.com/HaoxuanLiTHUAI/awesome_cognitive_and_neuroscience_skills
cp -r awesome_cognitive_and_neuroscience_skills/skills/optogenetics-protocol-designer ~/.claude/skills/
cp -r awesome_cognitive_and_neuroscience_skills/skills/research-literacy ~/.claude/skills/

    (Project-scoped alternative: copy into .claude/skills/ instead.)

No additional software is needed — this skill produces a protocol, not an analysis.

What it does

Works through six decisions:

  1. Manipulation type — fast (spike-locked) excitation, tonic excitation, sustained inhibition, phasic inhibition, or bidirectional control.
  2. Opsin selection — excitatory cation channels (ChR2 H134R, ChETA, Chronos, CheRiff, ChrimsonR, ChRmine, C1V1(TT)), inhibitory pumps and channels (eNpHR3.0, eArch3.0, stGtACR2, SwiChR++), or bistable step-function variants (SSFO, SOUL, SwiChR) for minutes-long state changes without continuous illumination.
  3. Light parameters — wavelength matched to the opsin’s action spectrum, irradiance set at the target depth after accounting for tissue scattering and absorption rather than at the fiber tip.
  4. Pulse protocol — pulse width, frequency and duty cycle kept inside the opsin’s channel kinetics, so the stimulation frequency you request is the firing rate you get.
  5. Fiber optics — core diameter, numerical aperture, and implant depth relative to the target, chosen together with the irradiance calculation.
  6. Controls — opsin-negative animals receiving identical light, off-spectrum wavelength controls, and within-subject light-off epochs.

Primary use cases: designing circuit-manipulation experiments in rodents, choosing between red-shifted and blue opsins for dual-color or deep-tissue work, specifying controls for a grant or protocol section.

Notes

AI-generated content — verify before use. The collection’s README states that all skills “were generated by AI from academic papers and other publicly available sources” and that “the content has not been individually verified by human domain experts.” This skill’s front-matter carries review_status: ai-generated. It cites Deisseroth 2015, Fenno/Yizhar/Deisseroth 2011, Yizhar et al. 2011, Mattis et al. 2012 and Aravanis et al. 2007. Opsin kinetics, irradiance thresholds and tissue-heating limits are experiment-critical and animal-welfare-relevant — confirm every number against the primary literature and your institution’s IACUC-approved protocol before use.

Sources

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