% Author: Lauren Jansen
% Name: ProPro.m
% Code takes tiffs thresholds and counts particles
% Data is exported into an excel file

%Image type: 1 Channel, 8-bit, 20X objective

% Updated 8/7/14

[filename, pathname] = uigetfile('*.*','MultiSelect','on');

m = cell(length(filename),2);
for i=1:length(filename)
    filenametemp = filename{i};
    B = imread(filenametemp); %reads the original files as images
    
    %convert the image to gray
    Image=rgb2gray(B);
    
    %Initially apply a Guassian filter to the image
    %# Create the gaussian filter with hsize = [5 5] and sigma = 2
    G = fspecial('gaussian',[5 5],2);
    %# Filter it
    Ig = imfilter(Image,G,'same');
    
    %Make image binary
    %The two different levels is another filter strategy
    BW2 = im2bw(Ig, 0.15);
    BW2_Opp=~BW2;
    
    %Apply another Gaussian Filter
    G2 = fspecial('gaussian',[7 7],3);
    Ig2 = imfilter(BW2_Opp,G2,'same');
    
    %Counts the nuclei in the image
    Bound2 = bwboundaries(Ig2);
    C2= num2str(length(Bound2));
    m(i,:)={filenametemp C2};
    
end

Out = input('Output filename? Format: enclosed in apostrophes Name.csv');
cell2csv(Out,m);