Split Stack resets coordinates?

[harrig12]

I have a SpatialData with two images, a and b. Each image is mapped to two coordinate system: global and aligned, with the following mapping:

a -> global: identity b -> global: identity a -> aligned: identity b -> aligned: affine

in the viewer, when I open the aligned images, things look good, but if I rightclick image b and use Split Stack to separate out the channels, then my aligned coordinated system seems to be ignored, and the channels all get reset to global. Mean (or other) projections don't seem to have this issue.

[LucaMarconato]

Hi, thanks for reporting.

@melonora do you know if there is a hook for Split Stack? I think that calling the function you wrote to transfer the metadata would fix this issue.

[melonora]

@harrig12 @LucaMarconato there is no callback other than a new layer being added as far as I know. However, we can potentially overload the call with the SpatialDataViewer class. I will look into it and report back / implement changes later this week. @harrig12 would you be able to share a small test example? No worries if you can't. One question what number of channels does B have?

[LucaMarconato]

Thanks a lot @melonora!

[harrig12]

Sure, here's an example zarr

splitstack_mwe.zarr.zip

The affine transformation on B is:

Affine (x, y -> x, y)
    [2.90898430e-01 6.02962457e-03 1.48529400e+02]
    [-2.58579771e-03  2.91931444e-01  2.53555781e+02]
    [0. 0. 1.]

In this example, I have 4 channels in B, but there may be anywhere from 1-40

Thanks! 💃

[melonora]

Thanks for providing the sample data! I will get on it

[melonora]

Hi @harrig12,

Just to give an update. I opened #136 to support multiple spatialdata objects. As a follow up PR I can fix the issue that you have as I have added a callback function when a layer gets inserted. Could you tell me whether you are using split rgb or split stack? Based on napari documentation these should behave differently.

Based on napari documentation:

Split RGB - if the image layer is an RGB image, it will be split into 3 new layers with red, green, and blue values in separate layers.

Split Stack - if an image layer is a stack (has 3 or more dimensions), it is split into a list of layers along the axis. This option takes a little time to execute. Properties will be changed as follows:

    - Colormap: (magenta, green) for a stack with 2 channels, (CYMRGB) for stacks with more than 2 channels

    - Blending: additive

    - Contrast_limits: min and max values of the layer

    - All other properties, such as Scale and Translate will be propagated from the original stack.

[harrig12]

I'm using split stack

[josenimo]

Hey spatialdata devs @melonora @LucaMarconato I report that this still happens on spatialdata 0.3.0 with napari-spatialdata 0.5.5

https://github.com/user-attachments/assets/3d786209-0319-4b40-bcb1-89f66c33df7f

Context: this is a subset (15 x 5000 x 5000) from a much larger sdata object (15, 44470, 73167). Not sure why the image goes far top left. Cropping looked like this

[LucaMarconato]

Thanks for reporting. Apparently the transformation metadata is lost for the newly created layer. We should check if there is a callback in napari we can use to update the metadata.