Simulation scripts

Repository simulations and figure generators live in scripts/. Run them as modules from the repository root so package imports resolve. Their opening docstrings describe inputs, calculations, and outputs. Generated data and figures belong in ignored diagnostics/ directories.

uv run python -m scripts.opm_simulation --output diagnostics/meridian_sphere
uv run --with matplotlib python -m scripts.plot_opm_simulation diagnostics/meridian_sphere/scan_0.2um

Workflow	Description
Meridian sphere	Known fluorescent object, optical forward model, and camera sampling
Publication figure	Acquisition and reconstruction panels at multiple scan spacings
Fixed-plane series	Object passage through a stationary oblique plane

Each workflow page records the physical assumptions and commands used for its figures. Experimental outcomes apply to those specified models and sampling; they do not establish performance for every specimen or optical mismatch.