about Interactive(sdata)

[szy23333]

...zarr_path = "./Xenium_V1_humanLung_Cancer_FFPE_outs.zarr"
from spatialdata import SpatialData

from napari_spatialdata import Interactive

if name == "main":
sdata = SpatialData.read(zarr_path) # Change this path!
i = Interactive(sdata)
i

[szy23333]

Why are there no images in the interactive interface?

[LucaMarconato]

Hi @szy23333, please select the coordinate system global, and then double click on the images you would like to visualize. This can be automated programmatically as shown in the code below:

from napari_spatialdata import Interactive

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

which is taken from this notebook . Please find more details there.

Also please check the documentation notebooks for napari-spatialdata here: https://spatialdata.scverse.org/projects/napari/en/latest/notebooks/spatialdata.html.