[QST] Question About When to Use rsc.get.anndata_to_CPU()

[YihengJiang0912]

What is your question?

Thank you for providing this amazing tool! It is incredibly useful. I am new to working with GPUs and would like some clarification on when to use the rsc.get.anndata_to_CPU() function.

While following the seuratv3-brain-1M notebook, I noticed that rsc.get.anndata_to_CPU() is used before calling rsc.pp.regress_out() and rsc.pp.neighbors(). Does this mean that if I want to use rsc.pp.bbknn() after rsc.pp.pca(), I should also call rsc.get.anndata_to_CPU() beforehand?

[Intron7]

@YihengJiang0912 sorry for the delayed reply!

If you have enough memory available, you generally don’t need to call rsc.get.anndata_to_CPU(). However, it's often best practice to run it after PCA. You may also need to run it before any visualization steps to ensure everything displays properly.

Let me know if you have any other questions!