make multicolor images

[mezwick]

Thanks for all your work on spatialdata and napari viewer.

Unless i have missed it, one missing aspect i would like is the ability to make multicolor images of image elemtns in spatialdata objects, within the spatial-data napari viewer plugin. So far as i can tell, this is not possible.

Expected behaviour

1. Load spatial data in napari with spatialdata plugin
2. Select coordinate system, load image element
3. Select a channel, adjust colormap and contrast limits
4. Select another channel, repeat step 3 until showing all channels as one would like
5. Have multichannel view of image, on which can overlay mask elements

Issue
Selecting a second channel, resets the whole image. Can only view one image at a time

Potential solutions
Option to load channels as individual image layers?

[LucaMarconato]

Thanks @mezwick for reporting this. @melonora @kevinyamauchi @Czaki does napari support this or is this in the roadmap? What do you think about the workaround? Thanks!

[mezwick]

Just to add in case useful for others. My current workaround is to load channels into sdata objects as individual images. Though this gets cumbersome for 40 channel high-plex images

[LucaMarconato]

Thanks for sharing your workaround. Maybe you'll find the code below useful. It can be used to programmatically set a colormap, and it could be extended for other settings, like contrast limits.

# the 'rasterize_002um' image, and the `new_cmap` variable have been created ealier in the notebook
# below we open napari in headless-mode and preload a layer, then we programmatically set a custom colormap

from napari.utils.colormaps import Colormap
from napari_spatialdata import Interactive

napari_cmap = Colormap(new_cmap.colors, "viridis_zero_transparent")

interactive = Interactive(sdata, headless=True)
interactive.add_element(f"rasterized_002um", "global", view_element_system=True)
interactive.get_layer(f"rasterized_002um").colormap = napari_cmap
interactive.run()

The code is from the Visium HD notebook (at the end).