Saving merged stacks

Hello there. I have two separated stack files that correspond to the green and red channels of a same acquired stack. What I want is to merge and save them in order to watch in the same file the green and red signal.
What I have done so far is to open the two separated files go to Image>Color>Merge Channels, and select each stack file for the respective red and green channels. The resulting composite looks fine, but when I try to save it either in .tif or .gif format what I get is a file that displays separately the slices from the green and the red stacks (slice1 green, slice1 red, slice2 green, slice2 red, …ad infinitum) and all of them in just one color -all images in green or all in red.
I’m sure there is an easy way to do this but I can’t find it out there. Any suggestions? Thank you very much.

Good day,

please study the relevant sections of the ImageJ user guide:

If problems persist, please post again.



Hello Herbie, thank you for your answer.
I had already read the information about stacks included in the guide that you sent me, the ImageJ wiki page on Stack Manipulation and different entries on this forum. And I still don’t know how to solve my problem -maybe I’m approaching it wrong from the start.

One way you could try is to make a stack of RGB slices which implies adding an empty blue channel.



Here is a ImageJ demo macro that does what you want. It requires the ImageJ-plugin “Stack_Interleaver”:

// imagej-macro "interleave stacks" (Herbie G., 25. March 2018)
// start generation of two stacks
run("Confocal Series (2.2MB)");
path= getDirectory("temp")+getTitle();
run("Bio-Formats Importer", "open="+path+" color_mode=Default split_channels view=[Standard ImageJ] stack_order=Default");
// start interleaving of two stacks
run("Stack Interleaver", "stack_1=[confocal-series.tif - C=0] stack_2=[confocal-series.tif - C=1]");
run("Stack to Hyperstack...", "order=xyczt(default) channels=2 slices=25 frames=1 display=Color");
selectWindow("Combined Stacks");
// imagej-macro "interleave stacks" (Herbie G., 25. March 2018)

Paste the above macro code to an empty macro window (Plugins >> New >> Macro) and run it.
(You need an open internet connection to load the demo image [first part].)



Thank you very much for your help! I think that I was not “activating” the composite that I created when merging/overlaying the two stacks, so when I saved the composite it was displayed as separated stacks. Don’t know if that makes sense.

However, I will try your demo and what you told me in the previous reply, and I will let you know. Thank you so much!