QuPath: overlay opacity without alignment

Hello everyone,
I faced similar problems as @Mike_Nelson in this post alignment brightfield fluo .
I have a brightfield image and the corresponding pseudo fluorescent one. The images have the same pixel size but I cannot align them (“this method is not supported by this color model”). Is there a way to use the overlay opacity without aligning on QuPath ? This would be very helpful to draw some ROIs and check classifications.
Has someone managed to do this ?
Thank you in advance !

How was this generated?

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Yes, the type of IF file was the issue in my case, was resaving as an OME-TIFF not an option there? Or could you start with an OME-TIFF (exporting through QuPath)?

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Thank you for your replies. It was generated on ImageJ (SIFT alignment, averaging some channels, stacking the images and applying LUTs). I can provide one and the corresponding brightfield one if needed.

I didn’t think of reexporting to OME-TIFF. I will try!

Are you unable to export it as an OME-TIFF? I am trying to understand why the previous resolution of the problem is not working in this case - the only issue I had there was the file size was too large for FIJI, which does not sound like it is the case for you.

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Yes, if you can example images that would help me figure out what is going wrong.

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Thank you very much @Mike, converting to Ome.tiff works (but I still cannot perform the alignment though).
I’m putting some examples just in case:
example_images_opacity.zip (3.4 MB)

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Once I converted the IF file to OME-TIFF it worked for me.

Hi, there should be no need to convert to OME-TIFF if you just select ‘Bio-Formats builder’ as the ‘Image provider’ when importing the composite image to a QuPath project.

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I’ve made a proposed fix at Use ColorModelFactory with ImageJ images · petebankhead/qupath@402f551 · GitHub that I hope will resolve the issue in the next version, so using the default image provider no longer throws an exception.

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