Overlay mask on to original image

Hi - Coming to the end of writing a script to first segment particles and then save each individually. Ideally I would only like the particle pixels (without background in boundary box) so I am attempting to create masks of each particle, overlay this, make each binary ROI (value of 0) 'transparent' so that the particle is on show with white (value of 1) surroundings - I have tried modifying other similar examples on here but none of them seem to work and the saved image is just the cropped image mask or a big white box ... any advice would be greatly appreciated.

%I = original image 
%binaryImage3 = logical mask created earlier on

    folder = 'c:/Users/ezxjp1/Documents/MATLAB/ParticleImages'

      for k = 1 : numberOfParticles          
          % Find the bounding box of each particle.
          thisParticleBoundingBox = particleMeasurements(k).BoundingBox;

          % Extract out this particle into it's own image.
          subImage = imcrop(I, thisParticleBoundingBox);

          % Create binary mask of subplot and overlay 
          subImageMask = imcrop(binaryImage3, thisParticleBoundingBox);
          subImageMaskUnit8 = im2uint8(subImageMask);

          % Get size of original image 
          [rowssubImage, colssubImage, numberOfColorChannelssubImage] = size(subImage); 
          [rowssubImageMaskUnit8, colssubImageMaskUnit8, numberOfColorChannelssubImageMaskUnit8] = size(subImageMaskUnit8); 

          % If size of mask does not match original, resize mask
      if rowssubImageMaskUnit8 ~= rowssubImage || colssubImage ~= colssubImageMaskUnit8 
          subImageMaskUnit8 = imresize(subImageMaskUnit8, [rowssubImage colssubImage]); 

      end

          Inew = subImage.*repmat(subImageMaskUnit8,[1,1,3]);

          pngFileName = sprintf('Particle_%d.png', k);
          fullFileName = fullfile(folder, pngFileName);
          saveas(gcf, fullFileName);
  end

[Guillaume]

I'm not really clear what it is you're trying to do. Presumably, your particleMeasurements come from regionprops, isn't what you want the Image property returned by regionprops?

Answer 1

[Image Analyst]

I have no time to dig into your code yet, but here's a few quick links that might help with overlays:

http://blogs.mathworks.com/steve/2009/02/18/image-overlay-using-transparency/

http://www.mathworks.com/matlabcentral/answers/104889-how-to-overlay-a-foreground-image-over-a-background-image