Q: How to render xenium morphology image with original colors?

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
python
Domain
data-visualization

Research direction

Start with the render_images call on morphology_focus and trace how its color arguments affect the plotted image. Compare the rendered colors with the Xenium Explorer reference values, and separately inspect how bounding_box_query uses the global coordinate system for the supplied physical coordinates. Done means the color behavior and coordinate conversion are documented or corrected with a reproducible example.

Written by the indexing model from the issue text.

Description

images :framed_picture: needs info priority: low

Hello @LucaMarconato!

Thank you very much for this tool. I want to plot a part of morphology image acquired with xenium + multimodal segmentation kit. It is loaded into spatialdata and plotted without errors, but the colors are dim and they are different from what I'd expected (DAPI - #0F73E6, Boundary - #F300A5, Interior RNA - #A4A400, interior protein - #008A00, reference values from Xenium Explorer). I tried passing a list of colors like this:

crop = lambda sdata: spatialdata.bounding_box_query(
    sdata,
    min_coordinate=[17_500, 55_000],
    max_coordinate=[19_500, 57_000],
    axes=("x", "y"),
    target_coordinate_system="global",
)

crop(sdata).pl.render_images("morphology_focus", ["#0F73E6", "#F300A5", "#A4A400", "#008A00"]).pl.show(
    ax=axes[0], title="Morphology image", coordinate_systems="global"
)

The code does not produce an error, it works twice as long, and it results in the same image with colors unchanged.

The key question is how to adjust the colors and saturation of the plot, so that it looked closer to what I see in Xenium Explorer?

Secondary question is how to translate physical coordinates into spatialdata's global coordinate system? Am I supposed to get transformation and then apply transformation to a single or a couple points to get min and max for cropping above? I can make a separate issue with this question, if necessary.

Best,
Vasily

Dominant language
Python
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Merged PRs (30d)
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