ExportToAnnData

[koalive]

Hi @bethac07 and friends!

I believe @timtreis already touched base about this: as part of a hackathon our team worked on a CellProfiler module to export results directly to AnnData and SpatialData formats, making it easy to use all of the single-cell tools from the scverse on morphological profiles.

We're wondering what would be the best way to distribute it while keeping things easy to maintain and update. Should we make a PR to this repo for instance?

For now, you can find our prototypes here (complete for AnnData, ongoing work for SpatialData): https://github.com/koalive/cp2ad/tree/main

Cheers!

[bethac07]

Hi Loan!

We're super excited you and Tim are working on this.

The short answer is "it's really up to you" - we'd be happy to host at least a copy of them here, that will increase their "discoverability" by people looking for other CellProfiler plugins (such as RunCellpose). Having your plugin here also reminds us that when we audit the plugins to see if any should be brought into the main program for CellProfiler 5, we remember to give it a look :) . We are happy for anyone to contribute here, and we distribute all plugins "as-is".

(Side note - we HOPE to make major changes to how Export modules work in CP5, which would make it much easier to "adopt" AnnData and SpatialData as first-class exports, but it's unclear if/when we'll get to it)

The downside from your perspective, of course, is that either a) you have two copies, and it's easier for them to diverge or b) all the work you're doing is in our org, not yours, so it might be harder for folks who are already using AnnData/SpatialData to "discover" these are now available from CellProfiler.

At the end of the day, CellProfiler just needs to know where the plugin is on the local machine, so totally up to you where you think the best place to host online to make it easy for your target users to find it and clone/download it.