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qupath / qupath-extension-bioimageio

A QuPath extension for working with the Bioimage Model Zoo (https://bioimage.io)
Apache License 2.0
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Error using the `Show test images in ImageJ` button #5

Open IvanHCenalmor opened 1 year ago

IvanHCenalmor commented 1 year ago

Hi @petebankhead , I was testing the Bioimage Model Zoo extension and I have had an issue while using the Show test images in ImageJ button.

I have used the 2D UNet nucleid broad model to test the extension and using the default values, when using the Show test images in ImageJ button the output that I receive in ImageJ is:

image

The target image is uploaded as a 256x2 pixel image with 256 channels, instead of what I suppose that it should be a 256x256 pixel image with 2 channels. Therefore, as the comparison between target and prediction images cannot be done, I suppose that might be the reason why no difference image is neither loaded.

If you need more information or anything, let me know. Iván

petebankhead commented 1 year ago

Hi @IvanHCenalmor I can replicate this. Will need to investigate - it seems to be because the NumPy dimensions are especially awkward (I think 1, 2, 256, 256) and it seems we don't handle that yet.