If you intend to use the colors for presentation purpose, you can you can use adobe photoshop and use different colors for different organelles.

Conversely, The image J software helps you analyze digital images using the RBG scale. (Red, Blue, Green)

I tried LUT in ImageJ, but it does not give a distinctive differentiation among organelles.

If you would like to have images like those in attached publication I am sorry to say that you have to "colour in" your different organelles manually with a suitable software e.g. Amira. This is then called segmentation and there are no good automatic routines to do that, all tedious manual labour!