Add qupath export bulk annotations update readme

[DanielaSchacherer]

• added qupath export to microscopy ANN notebook
• updated pathomics README

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fedorov commented on 2025-10-27T18:59:33Z
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Prefer to keep the output here

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fedorov commented on 2025-10-27T18:59:34Z
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I would strongly prefer to keep the output image panel here!

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fedorov commented on 2025-10-27T18:59:34Z
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I had to download that image and open in full resolution to see the annotations, since they are in red, and blend with the image. Is it possible to show those in yellow?

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fedorov commented on 2025-10-27T18:59:34Z ----------------------------------------------------------------

I had to download that image and open in full resolution to see the annotations, since they are in red, and blend with the image. Is it possible to show those in yellow?

It is in general possible if you generate annotations yourself. I remember that it was not easily possible in this case (couldn't figure out the reason) and decided that red is not optimal but good enough for the purpose here.
If it's okay with you, I would keep it that way for the sake of time.

[fedorov]

It is in general possible if you generate annotations yourself. I remember that it was not easily possible in this case (couldn't figure out the reason) and decided that red is not optimal but good enough for the purpose here.
If it's okay with you, I would keep it that way for the sake of time.

I have to say this is really unfortunate. It is hard to see red over a shade of red... But I didn't want to hold this PR for this reason.