Stitching hyperstacks

Hi everyone!

I’ve made several fluorescent pictures from mouse hippocampus (three channels: 647, 555 and 488 nm) and now I’d like to combine these by stitching. The pictures are in .czi-format, which contains the x and y coordinates for all the three channels and are opened as a hyperstack. I’ve tried using several of the stitching plugins, but I don’t seem to be able to stitch the images together without also merging all channels into one.
Instead, I’d like to end up with a new stack that contains the three separate channels as well. There is one very clear channel that could be the basis for the stitching algorithm, but this algorithm should then also automatically be applied to the other two channels.

I’m quite new to ImageJ/Fiji, so I hope this is clear enough. Thanks in advance!

Hello. It’s more helpful to let the forum know exactly what you’ve tried (preferably in nauseating amounts of detail).

I’ve had lots of success with the Grid/Collection stitcher that comes bundled with Fiji. You can select which channel to use for stitching (or an average) and it will maintain your three channels after fusion.

Hope that helps!

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Thanks for the reply!

I managed to get it working. The trick was to let Grid/Collection stitcher save the files to the disk, rather than to ‘fuze and display’.
The only downside to this is that I end up with a separate file for each of the three channels in my folder, which I then have to merge again using ‘Image - Stacks - Images to Stack’ to end up with a single file containing all three channels. I would imagine there’d be an easier option, but at least it works!