Fusion of multi-channel images


I acquired several 5-channel images in different positions(frames) and since these positions have almost no overlap I wasn’t able to work any of the automated stitching algorithms. I wish to fuse them into one large image manually but the mosaicj appears to work only with one channel. Is there any way to make this work so that I will have the fused image and retain all the channel information for analysis?



Did you acquire these images as tile scan ?
If yes, then when opening them with bioformats you should be able to “stitch” them.

If you can include the positions in the file name, I have had some luck with

using the “Stitch Grid of Images.” Even when there was no overlap, you just build the image using the order in which the images are added to the grid. You may need to create extra “blank” tiles to fill in spots if you don’t have a rectangular image.

Another option is following the recommendation for stitching multichannel images on the mosaicj help page:
“The [{Activate/Deactivate} Log File] menu determines if the operations applied to the tiles should be recorded in a file when the final mosaic is created. Before the log file is activated, like in Figure 3, no file is created. Once logging is activated, the menu switches to [Deactivate Log File] . In this condition, upon creation of the final mosaic, the user is given the opportunity to save a text file that will contain the operations performed to create the mosaic. These operations can be reapplied to recreate the same mosaic. Another use emerges if the log file is edited before it is reapplied; this allows one to process multichannel images, for example, by changing the source of the tiles.”

You would be stitching each channel with a separate step, but the calculations would all only be done once so the channels should line up. Not hugely efficient, but workable.

Thanks for the suggestion,

I was able to use the mosaicJ as suggested and can see the log file, but just couldn’t find a way to re-apply it to other images. Is there a tutorial of what to do that?

Thanks again,


The samples are actually several frames, each is a tile scan. Stitching the tiles themselves was simple, but fusing the different frames was challenging.



That I don’t know, unfortunately. Never used it. Adding the FIJI tag to this thread in case someone from that forum knows anything.

Actually, it looks like just below the part I linked has:

The menu [Replay from Log…] can be used to recreate a mosaic from a log file (see [{Activate/Deactivate} Log File…] ). It is accessible only when the upper section of the workspace contains no tiles.

Editing the correct channel might take some trial and error.

Awesome! it works!

Thank a lot,