How to stitch composite images on Fiji while preserving different channels (and not creating an RGB)

Hello Everyone,

Thanks in advance if you offer help, this website has been tremendously helpful in figuring out image processing.

So, I would like to stitch two maximum intensity projection CZI files, uploaded onto FIJI using Bio-format. I have attached them here:
41-17bL_bottom_MIP.czi (4.1 MB)
41-17bL_top_MIP.czi (4.1 MB)

Thanks to you all, I figured out how to keep my 4 channels separate in Image J. However, after stitching together two images, they seem to form 1 RGB image (it will say it has 4 channels, but it’s really just 1- and the colors seem seemed up. For example, DAPI will now look red instead of blue).

I would like to stitch them together, based on just DAPI for example – and then be able to open the stitched image back on ZEN blue, with my four distinct channels intact so I could do my analysis of each channel there.

Can anyone help me figure out how to accomplish that? Or any software recommendations for doing that in an easier way? Thanks!!

Laura C

Is there any reason you are not tiling these in Zen and stitching them there? I usually handle all of that in the native software/format, and then do additional processing/analysis in FIJI/QuPath.

I wish I could! I thought you could only stitch in zen if you had a motorized stage. Although perhaps that was an old post, I will look it up again.