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almaan / stereoscope

Spatial mapping of cell types by integration of transcriptomics data
MIT License
87 stars 26 forks source link

anndata support? #4

Closed giovp closed 4 years ago

giovp commented 4 years ago

Hi Alma,

Hope to find you well !

we recently finalized support for visium in anndata. You can have a look at how to analyse visium data with scanpy+anndata here and here.

We are planned to release a new scanpy version by end of the week, so online docs will be updated by then. Meanwhile, you can have a look at how visium is stored in anndata here.

I was wondering, do you still plan to provide anndata support for stereoscope? If yes, in what form? I was wondering whether having a basic API that allows users to run stereoscope from a notebook would make sense (essentially having stereoscope fully integrated in a scanpy pipeline).

Let me know what you think! Happy to contribute on this!

Best, Giovanni

almaan commented 4 years ago

Hi Giovanni!

That's great to hear! Stoked that Visium data is now compatible with anndata - and also interesting to see how you've approached how to keep multiple sections in the same anndata object! Also, thank you for the links - very informative.

To address you questions, yes this is very much on the todo list; my aim is to make stereoscope fully compatible with anndata files and also provide an API. I have some other projects that require my attention during May, but my estimate is that the anndata support/API should be in place by early June. I will for sure come back to you if there are any questions or such during that period!

giovp commented 4 years ago

That's great! Thanks a lot and again happy to help in any way!