Superimposing

Sounds like a job for layer masks.

On your layers, go to layer>add layer mask>reveal all.

Select black as the foreground color.

With the brush tool, select the mask, and paint out the areas of the layer that you dont want to see. White reveals, Black conceals.

I’m wondering if the new PS CS photomerge automation might work. That tool is intended to be used to build a seamless panorama from two or more images having similar overlapping edges. What you want to use from the photomerge tool is the ability to align the images and store each image on a separate layer.

I don’t know what photomerge looks for to align photos or how different the content can before it won’t align. But if each image, in your case, photos of the exact same cell, each with different hues, has similar content on an edge, it might work.

Not to broaden this topic, but your problem is sort of like superimposing over and underexposed photos and then blending the two (or more) to create an image with good highlights and shadows.

Another thing…I’ve seen plug-ins that allow a layer to be shifted by a fraction of a pixel. Supposedly, if the image source is from a film scanner, the images may need to be shifted by less than the one pixel movement that PS allows. By shifting one layer by a 1/3 of a pixel, the two images would be allowed to be superimposed exactly.