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