Hello,
I have one flourescence image. When opening the image in Fiji and qupath their channel information is different.
When opening the qupath image in fiji after sending it to fiji via the inbuilt extension channel information appears to be different as well. (same as in qupath)
qupath - channel order(1-4): red, green, blue, white
Fiji - channel order (1-4): white, red, blue, green
Am I missing something here?
What is the file type, what is the image server type QuPath is using (it is using ImageJ, BioFormats or Openslide, so one of those is picking your channel order), and how important is the false coloring of the channels? QuPath itself does not choose colors or channel order, that I know of.
Currently I think only BioFormats will allow you to recolor channels within QuPath.
Some more information here: https://github.com/qupath/qupath/wiki/Supported-image-formats
It turns out I had (at some point) set the server type to Bio-formats for tif images. That’s why. I reset it and am now using ImageJ server and my problem is solved.
Thank you!
