Artefact correction

Hi everyone, I’ve been working with TrakEM2 through ImageJ but I’ve come across some artefacts in the latest batch of images, like this one:

R2617_ZH9_CTR_0003.tif (1.3 MB)

is there a way to correct these based on the images on top/below? or at least delete the part of teh image so I can show the image below and try and make a contour? have been looking for a solution online but haven’t fopund one yet.

Thanks for your time!

@meperegri

Unfortunately, I don’t use TrackEM2 often enough myself to be of much help… but perhaps @bogovicj can get you on the right track? (get it?!)

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Hi @meperegri,

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,
John

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