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[ENH] Add various online datasources to the catalog (plugins)

Open edwardchalstrey1 opened this issue 3 years ago • 9 comments

Feature Request

Make various online data sources easily loadable via scivision

Describe the solution you'd like

Similar to #218 but for datasources instead of models

see: workshop notes

  • [ ] Write a "how to build a scivision plugin" tutorial for a new online datasource

edwardchalstrey1 avatar Apr 20 '22 14:04 edwardchalstrey1

These would be a good to add:

  • [ ] https://idr.openmicroscopy.org/cell/
  • [ ] https://www.rxrx.ai/rxrx1#the-data

quantumjot avatar Apr 22 '22 08:04 quantumjot

~~Also things like mnist - default image datasets~~ boring, let's stick to scientific imagery

edwardchalstrey1 avatar May 03 '22 10:05 edwardchalstrey1

  • Miquel's csv-image intake driver would allow a few to be added easily (e.g. from squidle)
  • Selected datasets from the Polar Data Centre (discussion with Paul B)

ots22 avatar Jun 22 '22 13:06 ots22

Earth Observation

acocac avatar Jun 22 '22 14:06 acocac

@quantumjot for the IDR data for example, what would you envision being in the scivision catalog? Do you think a catalog data entry that people can find via a query with a model trained on cell or tissue data, but which only has data for a specific example experiment would suffice? That way the user gets to discover the resource, and has some test data to play with, then they can go on to do things outside of scivision?

edwardchalstrey1 avatar Jul 07 '22 12:07 edwardchalstrey1

Idea from todays group session:

  • Add catalogs other than the default that come from online e.g. https://stacspec.org/en/tutorials/access-sentinel-2-data-aws/ which can be opened with: https://github.com/opendatacube/odc-stac
  • Would be great if there were similar examples from other domains

edwardchalstrey1 avatar Jul 20 '22 14:07 edwardchalstrey1

https://iiif.io/

edwardchalstrey1 avatar Jul 20 '22 14:07 edwardchalstrey1

another example: https://www.quantitative-plant.org/dataset

edwardchalstrey1 avatar Sep 20 '22 15:09 edwardchalstrey1

https://openorganelle.janelia.org/

ots22 avatar Nov 22 '22 12:11 ots22