Documentation hub for the OptoFly project. It covers the overall workflow, setup instructions, and consolidates documentation from the individual repos that make up the project.
Live site: https://mpinb.github.io/optofly-docs/
docs/overview.md,docs/workflow.md,docs/troubleshooting.md, anddocs/setup/*.mdare hand-written in this repo and explain how the pieces of the OptoFly ecosystem fit together.docs/repos/**is pulled in automatically at build/preview time byscripts/sync_repo_docs.pyfrom each component repo's own docs. It is never hand-edited here and is not committed (see.gitignore). If a component repo's docs are wrong or out of date, fix them in that repo — the next build picks up the fix automatically.
mpinb/optofly— the main real-time tracking and closed-loop optogenetic stimulation pipelinempinb/basler-charuco-calibrator— Basler camera intrinsic calibrationmpinb/liquid-lens-calibration— builds the liquid lens's z → diopter lookup tablempinb/optotune-lens— Python driver library for the Optotune liquid lens hardwarempinb/ximea-py— Python driver library for XIMEA camera hardware
pip install mkdocs-material
mkdocs serveThen open http://localhost:8000.
The site builds from docs/ using MkDocs Material and deploys automatically to
GitHub Pages on every push to main via .github/workflows/deploy-docs.yml.
See CLAUDE.md for conventions on structure, writing style, and how the
auto-synced docs/repos/** content works.
GPLv3 — see LICENSE.