% Author: Dr. Joshua Morgan and Isabella Bagdasarian, TIME lab, UCR
% perform a greedy segmentation of the nuclear channel
% uses a nuclei by nuclei threshold approach
%PARAMETERS
%           Do - NxN image (normally already filtered)
%           threshold- threshold parameter, single value 
%           areaopen- smallest size to preserve when performing bwareaopen,
%           single value

function [Db2] = GreedyNucSeg(Do, threshold, areaopen)

    Dbi = Do>threshold;
    Db1 = bwareaopen(Dbi,areaopen);
    CC = bwconncomp(Db1);
    Sn = regionprops(CC,Do,'MaxIntensity','MeanIntensity','PixelValues');
    L = labelmatrix(CC);
    Db2 = Db1;
    for si = 1:length(Sn)
        t1 = 0.05*Sn(si).MaxIntensity;
        Db2(L & Do<t1) = false;
    end
    
end