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https://xarray.dev
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[User story proposal] Xarray for Bioimaging #344

Open jhamman opened 1 year ago

jhamman commented 1 year ago

This is a proposal for a bioimaging use case story for Xarray. The story will be published on Xarray's blog (https://xarray.dev/blog).

Why?

Xarray is used in a number of bioimaing applications today (e.g. Allen SDK) and is a candidate data model / toolkit in a number of others (e.g. biohub, napari, etc.). A user story blog post showing how Xarray can be used to represent and analyze bioimaging data would help socialize the concept across the Xarray developer and bioimaging communities.

What?

We are targeting a short and non-technical post that illustrates how Xarray is (or could be) used in your bioimaging context. Below is a template outline that you should feel free to modify:

  1. Who am I?
  2. What problem am I trying to solve?
  3. How does Xarray help?
  4. Why did I choose Xarray?
  5. Current pain points (or ways that Xarray could better serve your use case)
  6. Technology I use around Xarray
  7. Anything else to know?
  8. Links and references

Feel free to insert images or short code blocks if they help you tell your story.

How?

Xarray's blog using Markdown with some front-matter. You can copy one of the existing posts to get started or you can write in a google-doc-like-thing and ask us to do the markdown formatting. If you copy a previous post, use a name like user-story-brain-imaging or whatever makes sense for your application.

xref: https://github.com/xarray-contrib/xarray.dev/issues/272

jhamman commented 1 year ago

@adamltyson, if you are up for it, here's a proposal for a blog post in your domain.

adamltyson commented 1 year ago

@jhamman in principle I'd be very happy to do this, but usage of xarray in our software is probably a few months away at this point.

jhamman commented 1 year ago

@adamltyson - sounds good. We'll check back early next year.

@jsiegle, @aamster, @danielsf - Would someone from the AllenSDK project be up for contributing here? We'd be interested in highlighting the use of Xarray within your project.

jsiegle commented 1 year ago

I'd be interested in writing something up, with the caveats that Xarray is only used in a very small part of the AllenSDK (the ecephys module), and it's used to represent voltage measurements (which are not technically bioimaging, because there's no light involved).

When are you hoping to have this by?

jhamman commented 1 year ago

Hi @jsiegle. Sorry to have missed your response. There is no specific timeline but we're ready whenever you are ready. Do you think you could have something ready by early December?

jsiegle commented 1 year ago

Yeah, that should work!

jhamman commented 1 year ago

@jsiegle - swinging back around to this. Are you still interested in writing something up?

jsiegle commented 1 year ago

Still interested! I should be able to get something to you by the end of Feb.