% Author: Dr. Joshua Morgan and Isabella Bagdasarian, TIME lab, UCR
% Watershedding is a technique that can be used to seperate
%clumps of objects by identifying local minima. This is especially useful
%for nuclei segmentation. 
%PARAMETERS
%           im - 2D logical to segment. 
%           threshold- threshold parameter, single value 

function [Dws] = NucWatershed_2D(im)

%watershedding
    ED = -bwdist(~im); %create a euler distance map (the distance from any pixel to the nearest background)
    %the minus sign converts each nuclear "hill" (since the center is furthest from the edge) to a "valley"
    ED(~im) = Inf;
    
    ED = imhmin(ED,1); %sometimes you can have 2 barely different minimas, the hmin will suppress any small minima
    Dws = watershed(ED); %watershedding associates each point with its nearest minima. Think of it like a drop of water hitting each pixel, which drops flow together?
    Dws(~im) = 0;
end