Here is a step-by-step guide that I made to help people export microscope images from ImageJ/FIJI and then import and alter colours/levels etc in Photoshop. The guide also shows you how to easily move from Photoshop to illustrator to make montage images etc for publication.
PDF Download: Guide to FIJI-Photoshop Image manipulation
Great news for those who cannot afford the very price commercial alternatives for 3D analysis of microscope images.
You can download the software here
And you can read the original research article published in Nature Protocols here