Multi channel composite z stack image xy shift/drift correction/alignment

[Jiseok]

Hello, I have a 3-channel composite, z-stack image like below.

There are two bars at the bottom of window for channel ‘c’ and z position ‘z’.
As you can see in the picture, green and blue channels are misaligned.
How can I nudge blue channel in xy direction to align with green, but do it for all z positions at the same time (same amount of nudging)?
I know how to nudge a single plane but I want to do it for all z planes at the same time.
Thank you!

[hwada]

Hi, Jiseok

There are some similar posts, so how about that as a reference?

Registering images from multiple cameras

@hwada: thanks for the suggestion! Given the misalignment I think I require AffineTransform though @bogovicj: thanks for the links and sample code! You’re absolutely right - adjusting to Dataset over ImagePlus (also figuring out how to handle RandomAccessibles to actually modify images) is definitely the challenge for me! I’ve managed to get a working script that, given a transform from Descriptor based registration and a single open stack, can transform all images in the stack: #@…

Struggling trying to align images using ImageJ

Hello, I am struggling trying to align several images using ImageJ. The images are the following: 4 images of the same spot in the tissue that belong to 4 different channels (blue, yellow, magenta and green) 2 images of the same spot but at different time point. In this case the staining for yellow is the same but green is different (magenta and blue are missing). I would like to align these 6 images together based on the alignment of the yellow channels since they are the same. The rest of…

I don’t mean to show off, but I recommend my plugin “CoordinateShift”, It seems to have your desired function.

hwada