This strikes me as more of a general image processing issue than a trakem2 specific thing.
Let me start by saying that if I was in your shoes, I would try to work around the artifacts rather than
trying to correct for them, but of course this depends on exactly what your analysis goals are.
That being said, what are your analysis goals?
Like you said, one approach would be to replace the values in the artifact areas with image data from an adjacent slice. If this is what you’d like to do, we can help you accomplish that, but I might recommend against it since it’s not correcting the artifact so much as it is changing the kind of artifact you have.
As far as I know, there are not specific tools in trakem2 or fiji to directly correct for artifacts like this.
This may be possible in trakem2 but I’ll have to look into it.
Sorry to not be of more concrete help,