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Non-RGB multichannels can be 3

Open aeisenbarth opened this issue 1 year ago • 16 comments

In pull request #115 for issue #66, a logic was implemented that converts multichannels to RGB if they are three.

In our use case, we have non-RGB channels, that can be 2, 4 or sometimes 3. The problem is that independent channels have very different value ranges and are not necessarily normalized, so that one RGB component is dominating. Furthermore, the visualization does not represent physical colors and can be misleading to the viewer.

image

Is there a way to set up the SpatialData object to explicitly use colors from the metadata, and avoid interpretation as RGB?

I think Napari's logic is that c must be 3 and additionally the order provided by the user must be yxc to interpret an image as RGB.

aeisenbarth avatar Aug 22 '23 07:08 aeisenbarth