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pachterlab / SpatialFeatureExperiment

Extension of SpatialExperiment with sf
https://pachterlab.github.io/SpatialFeatureExperiment
Artistic License 2.0
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Update `readXenium` for v2 output format #37

Closed lambdamoses closed 6 months ago

lambdamoses commented 7 months ago

See https://www.10xgenomics.com/datasets/preview-data-ffpe-human-lung-cancer-with-xenium-multimodal-cell-segmentation-1-standard

Good news: no more arrow binary for cell ID! Conversion of those is really slow, such a pain in the ass. The images are now different, with a morphology_focus directory with multiple images, probably from different z-planes. Need a way to determine the version, since for Xenium Onboard Analysis v2 I would prefer to read the parquet file.

lambdamoses commented 6 months ago

Also need to deal with multiple nuclei in one cell. I would need to wait for the release of v2 datasets, just to get the new label_id column which is required to make MULTIPOLYGON geometries from the nuclei.