As far as I know, nothing in MATLAB or IPT directly supports images with alpha, though you can certainly tote alpha around as a separate mask image. Even at that, imfuse() isn't a composition tool and has no means to utilize a mask.
% read images and alpha
[expr,~,expra] = imread('Expressions/standard.png');
[body,~,bodya] = imread('Body/maroon.png');
BG = imread('Background/blue.png');
% convert to floating point for simplicity
expr = im2double(expr);
expra = im2double(expra);
body = im2double(body);
bodya = im2double(bodya);
BG = im2double(BG);
% compose the image as weighted sums, working from the bottom up
outpict = body.*bodya + BG.*(1-bodya);
outpict = expr.*expra + outpict.*(1-expra);
% convert back to original class
outpict = im2uint8(outpict);
imshow(outpict)
MIMT has tools that can do this more succinctly, either using the alpha as a separate mask:
[expr,~,expra] = imread('Expressions/standard.png');
[body,~,bodya] = imread('Body/maroon.png');
BG = imread('Background/blue.png');
outpict = replacepixels(body,BG,bodya);
outpict = replacepixels(expr,outpict,expra);
imshow(outpict)
... or by using alpha combined with the image (RGBA)
[expr,~,expra] = imread('Expressions/standard.png');
[body,~,bodya] = imread('Body/maroon.png');
BG = imread('Background/blue.png');
% these are now RGBA images
expr = cat(3,expr,expra);
body = cat(3,body,bodya);
% imblend and imshow2 handle RGBA images just fine
outpict = imblend(body,BG,1,'normal');
outpict = imblend(expr,outpict,1,'normal');
imshow2(outpict)
... or the images can be combined as a layer stack and composed in a single pass:
[expr,~,expra] = imread('Expressions/standard.png');
[body,~,bodya] = imread('Body/maroon.png');
BG = imread('Background/blue.png');
% these are now RGBA images
expr = cat(3,expr,expra);
body = cat(3,body,bodya);
% pad and stack on dim4
stack = imstacker({expr,body,BG});
% compose the entire stack in one shot
outpict = mergedown(stack,1,'normal');
imshow2(outpict)
Though the latter two cases only makes sense if an RGBA workflow is convenient for other reasons. As I said, nothing in MATLAB or IPT knows what to do with an RGBA image, so you'd constantly have to work around that.
