superImp.m

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% Copyright (c) 2012, William E. Allen (we.allen@gmail.com)
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function im = superImp(c,frames,rad,maxVal,bb)
%%SUPERIMP combines multiple components into 1 image, assigning each
%%component a different color, for each pixel, choosing the component with
%%the largest magnitude at that location. All components are normalized.
%%INPUTS:   c = all 2-d image components
%%          frames = which components to combine in image (choose ones with well-defined features)
%%          rad = width of gaussian smoothing kernel
%%          maxVal = if you want to normalize all components by a fixed value (default: normalize maximum of each component to 1)
%%          bb = in case you want a separate background image to assign the intensity of the pixel, rather than the componnent

x = c(frames,:,:);

for i = 1:size(x,1)
    if rad
        x(i,:,:) = imfilter(squeeze(x(i,:,:)),fspecial('gaussian',5,rad));
    end
    if exist('maxVal','var')
        x(i,:,:) = x(i,:,:)/max(max(max(x(i,:,:))));
    else
        x(i,:,:) =  x(i,:,:)/maxVal;
    end
end
x = min(1,max(0,x));
[a b]= max(x);
a = squeeze(a); b = squeeze(b);
im = zeros(3,size(a,1),size(a,2));
for i = 1:size(x,1);
    im(1,b == i) = i/size(x,1);
    im(2,b == i) = 1;
    im(3,b == i) = a(b == i);
    if exist('bb','var')
        bb = squeeze(mean(bb));
        bb = bb-150;
        bb = bb./1500;bb = max(0,min(bb,1));%max(max(bb));
        im(3,b == i) = bb(b == i);
    end
end
im = max(0,im);
im = permute(im,[2 3 1]);
im = hsv2rgb(im);
figure;image(im);