Recommended approach for reading multiple Xenium slides with mutual panel at once #319
Description
We have an in-house developed visualisation platform that can import multiple spatial biology ROIs/slides for spatial transcriptomics assays such as 10x Visium and Xenium. The current spatialdata Visium reader is able to inherently support multiple Visium slides in one spatialdata zarr directory (and we have successfully rendered multiple Visiums in our software with this structure), but it appears that the Xenium spatialdata structure has one zarr store per slide/ROI.
We have a project comprised of multiple Xenium slides with a shared panel, and would like to have a streamlined approach for being to read all slides into our visualization software in one go. Is there a recommended approach for how to manage this? Would it make the most sense to read a directory of zarr sub-directories, parsing each sub-directories to look for a zarr store that has a Xenium slide? Or can the spatialdata/spatialdata-io API support multiple Xenium slides in one zarr.