%parameter file for matlab nuclear detection

MATLAB_STACK = true;

% common image configuration parammeters


slices=90; % # of slices in volume

xyres=.161; %voxel resolution (um)
zres=.5;  

%start and end time to be processed
start_time=1;
end_time=1;

% diameter of a nucleus at start time in pixels
firsttimestepdiam=20;

%guess at cell stage at start_time
%this is used only at the first time point to index into parameters when they are divided up by cell stage
firsttimestepnumcells=60; 

%turn on bottom detection
bottomdetection=true;



%main tunable parameters of algorithm
%this block of parameters can either be unstaged in which case each is set to a single number
%or they can be staged in which case staging defines which parameter setting is used for a given number of cells
% e.g. the 0-102 cells will use the first value in the array and so on. The setting arrays should have one more element than the stage array.


%stages (in number of cells) at which to switch between parameters that are arranged in blocks
parameters.staging=[80,102,181,251,351,400,550];


% threshold on noise maximas to discard the higher the number the more maxima will be discarded
%this is often the only parameter that needs to be changed to achieve good results in new images
parameters.intensitythreshold=[1,1,1.6,2,2,2,2,3];

%size filter used in terms of increments of expected diameter (usually 1, sometimes it is useful to set it lower in already blurry images)
parameters.sigma=1;



% threshold on slice inclusion in a nucleus, the bigger the number is the more likely it is to include ambigious slices in any potential nucleus
parameters.rangethreshold=[100,100,60,60,60,25,25,25];

% distance at which to merge overlapping nuclei (the larger it is the fewer nuclei will be detected)
parameters.nndist_merge=[.4,.4,.4,.4,.4,.3,.3,.3];
 
% mergescore above which consider merging if split is really bad (the lower (the more negative) it is the more merging will occur)
parameters.mergelower=[-50,-50,-50,-35,-20,-20,-20,-20];

%split score  below which consider merging nuclei even though merge score isnt so good (the higher it is the more merging will occur)
parameters.split=[20,20,20,19,17,10,10,10];

% merge overlappping nuclei if their merged aspect ratio is smaller than this
parameters.armerge=[1.2,1.2,1.2,1.2,1.1,.85,.85,.85];

%fraction by which split needs to be larger than merge to keep overlapping nuclei separate 
parameters.mergesplit=[1,1,.5,.5,.3,.5,.5,.5];

%fraction of maxima value on which slice rays will stop 
% at value .3 the boundary of nucleus is based on the isocontour representing 70 % of maximum intensity 
parameters.boundary_percent=.3;

%threshold on a boundary ray that is too much longer than its neighbor
parameters.large_ray_threshold=1.5;
%threshold on a boundary ray that is too much shorter than its neighbor
parameters.small_ray_threshold=1/3;


 
% internal program configuration parameters

downsampling=1;  % if set below 1 reduces image resolution to speed calculation



%ROI subergion for examination

%defines subregion of image (in original coordinate system) for processing 
%speeds up processing and allows multiple embryos to be processed 
ROI=false;

ROIxmin=0;
ROIxmax=0;

ROIymin=0;
ROIymax=0;

zeropadding=true; %time names do not have zero padding

%using  green and red side by side lsm images
newscope=false;
rednuclei=false; %nuclei are in green channel of 2 channel images

% name of trained disk inclusion distributions, would only change if you retrained model for new images
distribution_file='clean_distributions.mat';
distribution_file2='clean_distributions.mat';

%not using LSM files where all timepoints are all in one tiff 
LSM=false; %single volume lsm files


outputSlice=true;%output acetree readable slices for the images
savedata=false; %whether to save all partial results as well as final result in final mat file
SNoutput=true; %output nuclei/diameter text files 


%if a corrected answer is provdided this can be used to calculate accuracy online during detection, this will save to the mat file a variety of information useful for quantitatively tuning nucleus merging parameters 
nodata=true;%whether to use SN data to match online, 
nucleidir='G:\My Documents\latetest\';
embryonumber_ed='journalV_s1_edit';

nodatause=true;% obsolete whether to use SN data for diameter and stored bottom information
singlevolume=false; %obsolete flag that detects bottom on a per volume basis instead of at end of detection



newscope=false;

MATLAB_STACK=true;

%Parameter overwrites generated by ROI interface:

rednuclei=false;

start_time=1;

end_time=40;

outputSlice=true;

ROI=true;

ROIxmin=17;

ROIxmax=344;

ROIymin=11;

ROIymax=238;

ROIpoints=[17 11 ; 343 11 ; 344 237 ; 20 238 ; ];