Allow colormap scaling to reflect raw counts instead of hard-coded [0, 1] range

[lijinbio]

Hi there,

Currently, when visualizing gene expression or numerical observations in napari-spatialdata, the colormap and colorbar appear to be hard-coded to a range of $[0, 1]$. This is specifically seen in src/napari_spatialdata/_widgets.py (around line 488), where the data is normalized before being passed to the visualization layer.While normalization is useful for consistent styling, it makes it impossible for users to see the actual raw counts of a gene on the colorbar or via the contrast limits slider. For example, if a gene's expression ranges from 0 to 50, the colorbar still displays 0 to 1, and the user has no visual confirmation of the true expression magnitude.

I would like an option (or a change in default behavior) where:

1. The colormap scale and contrast limits are automatically set to (min, max) of the raw counts for the selected gene/variable.
2. The colorbar widget reflects these true values instead of the normalized $[0, 1]$ range.
3. Users can manually adjust these limits in the napari layer controls to values outside the $[0, 1]$ range if needed.

[LucaMarconato]

Hi, thanks for reporting. It's a bit hidden napari UI feature, but if you right click on the contrast limit slider you will be able to change limits. Did you try that?

Regarding an automatic limit based on min, max, it may slow down the interface for large non-raster, non-pyramidal data, so that would have to be considered carefully.

[lijinbio]

Hi @LucaMarconato , thank you for your suggestions. I just wanted to let you know that after following them, the right-click option does not show the limits to change.

[AlbertoFabbri93]

Is the contrast limit slider the one in the picture or? Because nothing happens when I change the range.

[LucaMarconato]

@lijinbio now I understood. I was referring to the "contrast limits" slider (for raster data), this one here:

@lijinbio @AlbertoFabbri93 the colorbar slider is not working, it's a known issue, it will be addressed in a future version #227