General information
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This simulation data belongs to the article:
Quantifying the minimum localization uncertainty of image scanning localization microscopy
DOI: https://doi.org/10.1016/j.bpr.2024.100143

Data availability
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The simulation code underlying the article can be found at:
https://github.com/qnano/spinflux-crlb

Data description
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The simulation data in this repository consists of a .zip file SimData.zip, containing all simulation data underlying the publication as .npy files.

Within SimData.zip, the title of each file contains simulated quantity and the simulation experiment it was obtained from. The data titles follow the following format (where the brackets <...> indicate variables):

<quantity><conditions><configuration><optional><scenario>.npy

The variables are defined as follows:
   - <quantity>: Name of the simulated quantity.
	* Bisum: Sum of pattern-(in)dependent background constants over ROI.
	* CRLBx: Cramér-Rao lower bound (CRLB).
	* EfBgsum: Illumination-intensity normalized total amount of background photons in ROI.
	* musum: Illumination-intensity normalized total amount of photons in region of interest (ROI).
	* Nmrange: Range of mesh pixel values Nm.
	* rlist: List of pinhole spacings r.
	* rplist: List of pinhole radii r_p.
	* signalsum: Illumination-intensity normalized total amount of signal photons in ROI.
	* slist: List of pinhole separations s.
	* thetablist: List of background photon count values thetab.
	* thetaIlist: List of signal photon budget values thetaI.
	* thetaIrange: Range of signal photon budget values thetaI.
	* xrange: Range of pattern focus x-positions.
	* yrange: Range of pattern focus y-positions.
   - <conditions>: Quantities that are varied in the simulation. This variable is not used for SMLM simulations.
	* _thetaI_Nm: Signal photon budget thetaI and mesh pixel values Nm.
	* _thetaI_thetab: Signal photon budget thetaI and background photon count values thetab.
	* _xp_r: Pattern focus x-positions and pinhole spacings r.
	* _xp_rp: Pattern focus x-positions and pinhole radii r_p.
	* _xp_s: Pattern focus x-positions and pinhole separations s.
	* _yp_rp: Pattern focus y-positions and pinhole radii r_p.
	* _yp_s: Pattern focus y-positions and pinhole separations s.
	* _yp_xs: Pattern focus x- and y-positions.
   - <configuration>: Configuration of pinholes and illumination patterns.
	* _SMLM: SMLM benchmark
	* _1pattern: single-pinhole, single-pattern configuration.
	* _2pattern: two-pinhole, two-pattern configuration where pinholes are separated along the x-axis.
	* _2pattern_rot: two-pinhole, two-pattern configuration where pinholes are separated along the y-axis.
	* _2pattern_nopinhole: two-pattern configuration without pinholes where patterns are separated along the x-axis.
	* _triangulation_rot_nocenter: equilateral triangle pinhole- and pattern configuration without a center pinhole.
	* _triangulation_nocenter: 90 degree clockwise-rotated equilateral triangle pinhole- and pattern configuration without a center pinhole.	
	* _triangulation_rot: equilateral triangle pinhole- and pattern configuration with a center pinhole.
	* _triangulation: 90 degree clockwise-rotated equilateral triangle pinhole- and pattern configuration with a center pinhole.
   - <optional>: Optional entry to specify a non-generic simulation condition:
	*_doughnut: a doughnut-shaped illumination pattern with a zero-intensity minimum was used in this simulation.
	*_ext: range of simulation variables was extended compared to other simulations.
	*_gt: Data attained with a dense-mesh pinhole approximation with 1000 mesh pixels per direction, assumed ground truth for discretization error analysis.
   - <scenario>: Description of the normalization constant, describing the simulated scenario of photon collection. This variable is not used for SMLM simulations.
	* No extension: Scenario where the illumination power and time are constant during illumination with all patterns.
	* _fb: Scenario where the entire signal photon budget is exhausted after illumination with the pattern (disregarding signal photons blocked by the spinning disk).
	* _adaptedbg: Scenario where the entire signal photon budget is exhausted after illumination with all patterns (disregarding signal photons blocked by the spinning disk), neglecting the effects of pattern-dependent background.

For example, the file CRLBx_xp_r_triangulation_rot_nocenter_ext_fb.npy contains the Cramér-Rao lower bound for the equilateral triangle pattern configuration without a center pinhole, simulated over a range of pinhole focus x-coordinates for various pinhole spacings r. The range of r was extended compared to other simulations, and the simulation considers the scenario where the entire signal photon budget is exhausted after illumination with the pattern (disregarding signal photons blocked by the spinning disk).

Using existing data
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This section describes how to use the simulation data in this repository to reproduce results.

1. Create a directory "/spinflux-crlb/SimData/".

2. Download SimData.zip from this repository. SimData.zip contains all simulation data underlying the publication.

3. Extract SimData.zip to the directory "/spinflux-crlb/SimData/".

4. Follow the instructions on reproducing the figures on https://github.com/qnano/spinflux-crlb.