Tiny bug in slide overview navigator

I’ve noticed in some .mrxs files, the rectangle that shows my FOV in the slide overview picture does not match where I’m actually looking. I will be centered on the tissue, but the red rectangle shows a completely different location. In this picture, the yellow circle shows what I’m actually looking at, but the red square is totally off.

This seems to get worse the further down the slide I am, almost like it isn’t scaled properly. It feels like for every pixel downwards I move in the overview scan, that rectangle moves 1.1 pixels, or something like that.

Oddly, if I click on a spot on the overview, it moves the slide correctly to be centered where I clicked, but the red rectangle is still wrong. So this is just about that rectangle to visualize the FOV. Also it doesn’t happen on every slide, but it consistently happens on the slides that have the issue. I’ve never noticed this problem before, but I’ve also never worked with images that are this elongated. It seems to happen in the Y direction more than the X, so maybe the total length or aspect ratio matters for some reason?

Note: this doesn’t affect my work at all and certainly isn’t worth bothering with. I just wanted to report it in case anyone else saw the same thing and thought they were crazy. QuPath 0.2.3 on Win10.


Hi @smcardle ,

That’s odd! I don’t think I’ve ever experienced this, thanks for flagging it.
Do you happen to have an example or two (free of permission/privacy issues) for us to reproduce the issue on our side?


I can’t post the files publicly, but I can email you directly a test file if that’s helpful.

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Sure, I’ll send you a private message now.

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