Fluorescence micrograph editing in ImageJ, Inkscape, or Gimp? - (May/18/2014 )

Hey guys, so I'm having some trouble editing micrographs for my figures in an upcoming paper.

We have cells with different regions fluorescing different colors, and my collaborator sent me the greyscale images of these cells. I know how to simply merge pseudocolor images by RGB channel, but the problem is the images I was sent aren't perfectly aligned. What I need is the ability to slide the two images over one another so that they are properly aligned. I have done this in the past, but I believe it was with native microscope software I no longer have access to. Do y'all know of a way for me to do this with ImageJ, Inkscape, or Gimp? Or do I need to have my collaborator mess with it with his software?

It's easy for me to adjust the opacity of one image and slide it over the other, but then I have to worry about how the background obscures the image I am merging into. Does this make sense? Thanks for any help.

No need to double post - I've deleted your other one.  Bob

You can do this in both ImageJ and Gimp - Inkscape is more for drawing and laying out images, it is not image manipulation software.

I prefer to do this in Gimp personally - just open the images you want (as RGB), copy one the images you want to overlay and paste it onto another one (e.g. if you had 3 images A, B, and C, then you could copy A onto C).  Now open the layers dialogue (Windows>Dockable dialogues>Layers) and click on the floating layer, this activates it for further manipulation.  Now select the Mode pull-down menu (at the top of the layers dialogue) and choose Difference, this should allow you to see the two layers superimposed.  You can now move the floating layer by using the arrow keys or mouse.  Repeat for the other images you want to overlay.