check out the newest calcium imaging data available from allen institute

[jovo]

http://observatory.brain-map.org/visualcoding

• [ ] report back here whether they have any 2d time-series data that is readily ingestable?

@kunallillaney

[Aeusman]

The data needs to be pulled using their python package. It's not particularly intuitive (no tutorial on how to just download image data), but I'll try to download some, see how far I get, and if I'm confused email them.

[Aeusman]

Do we currently have the data from NWB CRCNS datasets? @jovo - This seems like it might be more straightforward to ingest, but I would need a CRCNS account.

edit: Nevermind, they don't allow for 'redistribution of the data' : https://crcns.org/terms

[Aeusman]

I've tried to make sense of the allen institute data model and python package, but it is extremely confusing and badly documented (even after source diving): http://alleninstitute.github.io/AllenSDK/_static/examples/nb/brain_observatory.html#Download-Experiments-for-a-Container

Part of the challenge is the sheer amount of metadata associated with every dataset, much of which is not easily understandable. For example: [u'Cux2-CreERT2', u'Rbp4-Cre', u'Rorb-IRES2-Cre', u'Scnn1a-Tg3-Cre'] means absolutely nothing to me (from the notebook) but they are apparently the cre lines which are used to define experiment containers?

[jovo]

dunno. ask them?

On Tue, Jun 21, 2016 at 11:32 AM, Alex Eusman [email protected] wrote:

I've tried to make sense of the allen institute data model and python package, but it is extremely confusing and badly documented (even after source diving): http://alleninstitute.github.io/AllenSDK/_static/examples/nb/brain_observatory.html#Download-Experiments-for-a-Container

Part of the challenge is the sheer amount of metadata associated with every dataset, much of which is not easily understandable. For example: [u'Cux2-CreERT2', u'Rbp4-Cre', u'Rorb-IRES2-Cre', u'Scnn1a-Tg3-Cre'] means absolutely nothing to me (from the notebook)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/neurodata/ndstore/issues/291#issuecomment-227478432, or mute the thread https://github.com/notifications/unsubscribe/AACjcj8iaADk_mP3AVXPBN4m1Gw-xEZLks5qOAQpgaJpZM4I2xaP .

the glass is all full: half water, half air. neurodata.io, jovo calendar https://calendar.google.com/calendar/embed?src=joshuav%40gmail.com&ctz=America/New_York

[Aeusman]

I contacted them yesterday, waiting on a response

[Aeusman]

This is sitting on bg1, but cannot be ingested yet due to the same issue with codeneuro.

[jovo]

@kunallillaney @randalburns @Aeusman ok, we gotta support 2D time-series data. let's discuss priorities on wednesday.