Repository navigation
Is it possible to show two different channels of the same image as different layers? #351
Description
I am experimenting with a Xenium dataset that was run with the cell segmentation staining kit.
This result in a Spatialdata object with an image element morphology_focus with the channels for the different segmenation stains.
See above (5) the different channels of the image.
What works adding the same image channels as two separate layers ((1),(2)) with different colormaps (4) and making a comosite by adjusting translucence (3)
What I did not figure out Showing two different channels
When I change they channel of one layer (5) the other layer also automatically switches to the same channel.
Is there a way to do this?
Activity
MSHelm commentedon Feb 27, 2026
I also ran into the same issue recently. I have basically the same setup, where I want to check the overlap of 2 different channels (for example to check if a given cell expresses both markers). But as @pakiessling also mentioned, I cannot figure out how to overlay 2 different channels. This would really be a good feature for visual inspection.
LucaMarconato commentedon Mar 1, 2026
There was some preliminary work done here from @melonora #365; it should be already usable but it requires rework before merging (described in the comment).
But there is an update: IIRC there will be some new feature in napari to select and color channels independently. @melonora do you info on the timeline/point to a PR please?