spatialdata_io.xenium() assumes the dataset contains both nucleus and cell segmentation masks as in the standard Xenium structure. E.g. Proseg-imported segmentation only contains a single segmentation mask and therefore cant be loaded properly. Also setting
cells_labels=False
nucleus_boundaries=False
does not solve the issue.
spatialdata_io.xenium() assumes the dataset contains both nucleus and cell segmentation masks as in the standard Xenium structure. E.g. Proseg-imported segmentation only contains a single segmentation mask and therefore cant be loaded properly. Also setting
cells_labels=False
nucleus_boundaries=False
does not solve the issue.