OptoFly Ecosystem Wiki
This is the documentation hub for the OptoFly project: a real-time tracking and closed-loop optogenetic stimulation system for flying insects, plus the calibration tools it depends on.
If you're setting up a new rig or working on this project for the first time, start here:
- Read Overview to understand what the pieces are and how they fit together.
- Follow Setup → Environment first, then see Workflow for which tool to set up in which order.
- Read Workflow for the full calibration-to-experiment pipeline, in order.
If something isn't working, check Troubleshooting first.
The repos
| Repo | What it does |
|---|---|
optofly |
The main pipeline: real-time fly tracking, triggered recording, optogenetic stimulation, autofocus, visual stimuli |
basler-charuco-calibrator |
One-time camera intrinsic calibration for each Basler tracking camera |
liquid-lens-calibration |
Builds the lookup table the liquid lens uses to autofocus at a given distance |
optotune-lens |
The low-level driver library both optofly and liquid-lens-calibration use to talk to the liquid lens hardware |
ximea-py |
The driver library liquid-lens-calibration uses to talk to the XIMEA focus camera |
braid-opto-power-measure |
Occasional QC check: maps optogenetic LED power/irradiance across the arena |
optofly-analysis |
Post-hoc analysis of finished recordings: behavior stats and stimulus/optogenetic response |
Full docs for each are under Component Docs
in the sidebar — this wiki pulls them in automatically so they're always
up to date with each repo's own main branch.