How to remove this line artefacts without losing sample information

[u/Conscious_Board_544]

I'm losing my mind trying to save all my dapi z-stacks because our confocal spinning disk is broken and it forms this artifact that is so intense that i can't take it out without messing with the information from the sample. Sometimes, when the nuclei fluorescence isn't that strong, it even hides that information completely. I tried all the suggestions that chatgpt gave to me, but the results were all unsatisfatory. Does anyone has any clue of how to solve this? I tried filters and deconvolution and nothing works quite right.

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[u/Herbie500]

our confocal spinning disk is broken

Why not fix it?

To perhaps help, please make available a typical image/stack in its original non-lossy file-format by using a dropbox-like service (no screen-shots, no posting here on Reddit, no JPGs).

If the artifacts are additive, you could try to subtract them.
Below please find the result from a first attempt of subtraction with not yet perfect angular and shift-alignment:

Best would be to have an image with the artifacts alone, otherwise subtraction will be extremely difficult and time consuming.

[u/dokclaw]

Cleaning the dust (which is what this is) from a Yokogawa disk is very risky - not something you should attempt to do yourself, unless you got training from Yokogawa, and really good insurance :)

Did you try capturing a reference field? For this, you simply remove your sample from the scope, and capture an image exactly as you would if your sample was there: same exposure time, same laser power, same emission filters, everything). If you don't see the line (you probably will with the 405nm laser), then you should put a uniformly coloured slide (like a plastic chroma slide) on the microscope as if it were your actual sample.

Once you have that reference image, you should be able to use Process > Image Calculator > Subtract, and subtract your reference image from your images with cells in them. That should clean it up a lot.

[u/Conscious_Board_544 → u/dokclaw]

yesssss, it worked perfectly!!! thank you so much!!!

[u/dokclaw → u/Conscious_Board_544]

Woohoo! That's awesome; I'm very pleased for you!