[Bug]No neighborhood Data in h5ad-files?

BodenmillerGroup / steinbock

A toolkit for processing multiplexed tissue images

https://bodenmillergroup.github.io/steinbock

MIT License

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[Bug]No neighborhood Data in h5ad-files? #210

Open albert180 opened 1 year ago

albert180 commented 1 year ago

Hi, when exploring the .h5ad-file generated by steinbock export anndata --intensities intensities --data regionprops --neighbors neighbors -o objects.h5ad I've noticed that it doesn't contain any neighborhood-data. There exists a neighbors folder generated by Steinbock, and when using the read_steinbock()-function of imcRtools, the neighborhood-Data is included correctly in the SPE. grafik

jwindhager commented 1 year ago

I've also reported this here: https://github.com/BodenmillerGroup/steinbock/issues/196