For your second image and the images you have posted earlier, finding number of particles and measuring their intensity is a simple matter (search: Imagej particle analysis).
However, in the more crowded image you posted it looks like the particles are piled up, or forming aggregates, distinguishing these could be very hard, if possible at all. If they are indeed in a pile on top of one another you would need a 3d scan to separate objects?
But if you are sure that the particles are not stacked then maybe an automated threshold and watershed could suffice. Possibly a trained WEKA classifier for more robust analysis. Maybe you have some expert advice @etarena or @iarganda, can this densely populated image be realistically segmented?
In any case the analysis will not be perfect, what degree of accuracy do you require for these experiments? If you are just say, comparing the two images in your last post then we can of course plainly see the significant difference. Comparing two densely populated images to one another is a different matter..