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laminlabs / lamindb

A data framework for biology.
https://docs.lamin.ai
Apache License 2.0
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SpatialData support: roadmap #1533

Open srivarra opened 5 months ago

srivarra commented 5 months ago

Hello,

I've been going through the documentation and tutorials for lamindb and this is a very easy to use, and useful project. I plan on using it for my analysis work (Multiplexed imaging cancer data), and I would like to contribute as well. Specifically I'd like to help implement spatialdata support.

Let me know your thoughts!

falexwolf commented 5 months ago

Welcome @srivarra!

Yes, we're just launching the first piece of documentation for a vitessce export and will be supporting the spatial team at the Boston Hackathon.

We've also chatted about the topic with @giovp and @timtreis

Long story short: We're very happy if you help us build support and good documentation for SpatialData.

Do you happen to be at the Hackathon? If not, I suggest we get on a call to coordinate!

srivarra commented 5 months ago

@falexwolf Unfortunately I won't be able to attend the Boston hackathon, but I'm open to call!

falexwolf commented 5 months ago

Wrote you an email based on what I found on your GitHub profile to coordinate!

falexwolf commented 5 months ago

FYI @giovp @timtreis @chaichontat @Zethson @sunnyosun and anybody else reading this: @srivarra and I will coordinate on how to proceed today at 5 pm CET / 11 am EST / 8 am PST (2 hours from now).

If any of you want to join, you're welcome! Just ping me for the Zoom invite.

The rough agenda is to get a sense on what exactly @srivarra wants to contribute!

Given that LaminDB already supports arbitrary zarr stores, my sense is that it's validation that's aware of SpatialData. We'll figure it out in the meeting!

FYI: We're starting to track some examples here https://lamin.ai/scverse/spatial

They're right now primarily focused on AnnData zarr exports and Vitessce but this is not where it should end