Image rendering is very slow for xenium morphology image

[tsvvas]

Hello @LucaMarconato!

I noticed that rendering of xenium morphology images takes 10+ minutes each time. I run the code on a server and have enough memory to fit the image and required transformations. I tried selecting certain scale in the default multi-scale image as suggested in documentation, but that did not help accelerate rendering time. My expectation is that it should not take so long, given that Xenium Explorer can render the image on the fly on local computer.

What can I do to accelerate image rendering?

Best, Vasily

[LucaMarconato]

Hi, I believe that the problem can be solved by saving the SpatialData object to disk and reading it again, so that the Zarr optimizations are used.

If that is the case I would appreciate some feedback on where we could put this information to be discoverable. We placed it around the documentation and examples but it may not be enough. Thanks!

[tsvvas]

Thank you, Luca, this solution works for me.

I was looking for it in the optimizations section in spatialdata tutorials, but it is confusing to go back and forth between spatialdata and spatialdata-plot to look for information. I believe spatialdata-plot needs its own set of tutorials focused on visualization.

Best, Vasily