pixel average color - from http://pastebin.com/2tmcGPd8

color_average.m

function color_average(image,diameter,type,thresh)
%% image is the name of the file 'image.format'
%% diameter is the cell size
%% type: either 'circle' or 'square'
%% thresh: from 0 to 1. Size of the gap between cells

[colormat,~,~] = imread(image);
[x,y,z] = size(colormat);

rows = floor(x/diameter);
columns = floor(y/diameter);
out = zeros(rows,columns,3);


pre_image = ones(rows*diameter,columns*diameter,z);
for i = 1:rows
    for j = 1:columns
        
        r = mean(mean(colormat((i-1)*diameter+1:i*diameter,(j-1)*diameter+1:j*diameter,1)));
        g = mean(mean(colormat((i-1)*diameter+1:i*diameter,(j-1)*diameter+1:j*diameter,2)));
        b = mean(mean(colormat((i-1)*diameter+1:i*diameter,(j-1)*diameter+1:j*diameter,3)));
        
        midavgx = (i-1)*diameter+1 + diameter/2;
        midavgy = (j-1)*diameter+1 + diameter/2;
        
        if strcmpi(type,'circle')
            for I = (i-1)*diameter+1:i*diameter
                for J = (j-1)*diameter+1:j*diameter
                    
                    if sqrt(abs(I-midavgx)^2 + abs(J-midavgy)^2) < thresh/2*diameter
                        I;
                        J;
                        pre_image(I,J,1) = r/255;
                        pre_image(I,J,2) = g/255;
                        pre_image(I,J,3) = b/255;
                    end
                end
            end
        elseif strcmpi(type,'square')
            for I = (i-1)*diameter+1:i*diameter
                for J = (j-1)*diameter+1:j*diameter
                    if (abs(I-midavgx) < thresh/2*diameter) && (abs(J-midavgy) < thresh/2*diameter)
                        pre_image(I,J,1) = r/255;
                        pre_image(I,J,2) = g/255;
                        pre_image(I,J,3) = b/255;
                        
                    end
                end
            end
        end
            out(i,j,1) = round(r);
            out(i,j,2) = round(g);
            out(i,j,3) = round(b);
            
            
        end
    end
    
    imshow(pre_image)
    imwrite(pre_image,'output.png','png');
end