Table 1.

Simulator parameters.

Category	Parameter	Notation	Unit/format
Geometry	Reference image		.TIFF, PNG, JPG, GIF
	Image pixel size		µm/pixel
	Region file		.rgn or .roi
	FRAP laser spot		2.8 µm
	FCS laser spot width	σFCS	0.25 µm
Molecules	Numbera		1–150,000
	Initial position		Uniform or estimated
Times	Simulation durationa		1000–100,000 frames (40–1600 s)
	Time step	Δt	2–100 ms
Diffusion coefficients	Outside contact	Dout	0.3 µm2/s
	Inside contact	Din	0.3 µm2/s
	Trapped	Dtrap	0.04 µm2/s
	Crossing probability	Pcrossing	25–70%
Kinetics	Binding rate	kon	0.15 s−1
	Unbinding rate	koff	0.015 s−1
Photophysics	Switch-on ratea	konFluo	0.005–5 s−1
	Switch-off ratea	koffFluo	0–10 s−1
	Bleaching ratea	koffBleach	0.4–4 s−1
	Activation ratea	koffActiv	1–2 s−1
Export files	SPT or SRI images		.TIFF or multi-TIFF
	SPT trajectories		.trc
	SPT histogram		.txt
	FRAP curves		.txt
	FCS fluctuations and autocorrelation		.txt

^aSee the methods above for the specific molecule numbers and photo-physical parameters used in the various imaging modes (SPT, STORM, FRAP, PAF, FCS).