//Never set this to anything other than [1 1]
log_ratios_zoom=[1 1]

//Zoom level to use of debugging graphics are enabled
debug.zoom=4




//Transition matrix and initial probabilities
A=[0.16 0.84 0; 0.495 0.495 0.01; 0 0 1]
pi=[.5 .5 0]


//General parameters
gibbs.mixing_iterations=1
cg.max_motion=0.5

//Specific subsystem parameters

//Main optimization
main.optimization_version=2
main.cg.max_iterations=5
main.gibbs.samples=10
main.passes=4

//Stop the optimization if this many consecutive iterations
//have empty models (no spots). For 0 or less, it never stops
//on this criterion. 1 will stop at the first empty iteration.
main.consecutive_empty_models=0

///This is the minimum size for empty models
///At N or fewer spots, the model is considered to be empty.
main.empty_model.max_size=3



//Add - Remove
add_remove.optimizer.samples=20
add_remove.optimizer.attempts=10
add_remove.optimizer.hessian_inner_samples=1000


add_remove.thermo.samples=1000
add_remove.hessian.outer_samples=100
add_remove.hessian.inner_samples=1000
add_remove.tries=10



//Skip the preprocessing step (or now)
preprocess.skip=0
preprocess.fixed_scaling=0
//Low pass filter has this sigma
preprocess.lpf=5

//Threshold the log_ratios image at this leve;
threshold=0

//Dilate log_ratios imge by this radius after thresholding
radius=0

//Use marked region 19
cluster_to_show=19
//Actually, ignore that, simply use the largest marked region
use_largest=1

//Allow spots to be at most this far outside the marked region
position.extra_radius=2.3
//Use a uniform position prior (to make spot probability a proper distribution)
position.use_prior=1

//Scale the maximum step in brightness according to the prior shape
max_motion.use_brightness_std=1

//Options are: 
//  uniform (place spots uniformly over the area of interest)
//  intensity_sampled  (place spots more densely in brighter regions)
placement=intensity_sampled




////////////////////////////////////////////////////////////////////////////////
//
// Things you might want to change are below here
//

////////////////////////////////////////////
//
// Spot shape priors. Make sure you SET THIS correctly.
//
// calculating a value for blur.mu:
// 1. temp_sigma = (fwhm_in_nm / pixel_size_in_nm) / (2 * sqrt(2 * ln(2)))
// 2. blur_sigma = 0.1
// 3. blur.mu = ln(temp_sigma) + (blur_sigma * blur_sigma)
//

//Corresponds to 300nm at 100nm per pixel
blur.mu=0.252148
blur.sigma=0.1

//Corresponds to 300nm at 160nm per pixel
blur.mu=-0.217856
blur.sigma=0.1

//Corresponds to 270nm at 79nm per pixel
//blur.mu=0.38251
//blur.sigma=0.1

////////////////////////////////////////////
//
// Spot intensity priors. You can probably leave this as-is
//
intensity.rel_mu=2
intensity.rel_sigma=1


//Number of spots (for uniform and intensity_sampled). SET THIS
placement.uniform.num_spots=15




