Opening an ImageJ "Stack" in QuPath not recognizing channels


I have a newbie Qupath question. I can open a multichannel “component” image I acquired with a akoya polaris instrument:

(btw, Stardist with a model I trained worked great!)

In ImageJ I took that same image, split it into individual channels and saved those as tif. Later I made a “Stack” from some of the individual tif images then saved it as an 8-bit tif and opened that in Qupath. Why doesn’t Qupath recognize the stack is composed of different channels?

Thanks for the help! -John

When you saved it as a tiff you saved it as a Zstack. That is the default for an ImageJ stack. You will want to change that in the Image->Properties in imageJ…

A quick script will let you set all of the right values if you set macro record when doing it the first time. I would make sure the pixel size is correct as well.

ah, Image->Properties window… That works, thanks! -John

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This thread helped me with my analysis. Thank you.

One extra question: How can I make sure the pixel size is correct? By default I get these values with my samples:

Pixel width and height: 0.0000394
Voxel depth: 1


The correct pixel size is determined at the instrument. Generally it will be stored in the metadata, though older systems (or custom designs) may require calibration with a calibration slide to determine the actual pixel size.

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