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informatics-isi-edu / synspy

Synaptic segmentation and visualization with fluorescence microscopy
BSD 3-Clause "New" or "Revised" License
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Request type of fish #66

Closed aandreev0 closed 6 years ago

aandreev0 commented 6 years ago

Right now i don't have API access to type of experiment in cohort. That is, Bill sends me file that looks like:

Learners:
Dsy20160116A    -   6025        -   3 (stars)
Zdu20170516A    -   6483        -   3
Dsy20170316B    -   6493        -   4
Dsy20161202B    -   6791        -   3
Dsy20170316A    -   7949        -   4
Dsy20171019B    -   JK6     -   4
Dsy20170426A    -   R5Y     -   3*
Dsy20180404B    -   ZHT     -   4
Zdu20180404A    -   11YG        -   3
Zdu20180404B    -   11YR        -   4

Nonlearners:
Dsy20170329C    -   6479        -   4
Dsy20171019A    -   JKE     -   4
Dsy20170202A    -   7965        -   4
Dsy20170412A    -   6481        -   4
Zdu20171114B    -   JJE     -   3
Zdu20171020A    -   JJY     -   4
Zdu20171031A    -   JJP     -   3
Zdu20171121A    -   JJ6     -   4
Zdu20180403A    -   11Z0        -   3
Dsy20180404A    -   11Z8        -   3

I would like to be able to pull type of experiment from storage somehow using fish ID (not sure correct terminology) like "Dsy20160116A".

carlkesselman commented 6 years ago

That exists and I can give you code that will get this using the standard APIs. Let’s talk next week

Sent from my iPhone

On Aug 17, 2018, at 7:04 PM, aandreev notifications@github.com<mailto:notifications@github.com> wrote:

Right now i don't have API access to type of experiment in cohort. That is, Bill sends me file that looks like:

Learners: Dsy20160116A - 6025 - 3 (stars) Zdu20170516A - 6483 - 3 Dsy20170316B - 6493 - 4 Dsy20161202B - 6791 - 3 Dsy20170316A - 7949 - 4 Dsy20171019B - JK6 - 4 Dsy20170426A - R5Y - 3* Dsy20180404B - ZHT - 4 Zdu20180404A - 11YG - 3 Zdu20180404B - 11YR - 4

Nonlearners: Dsy20170329C - 6479 - 4 Dsy20171019A - JKE - 4 Dsy20170202A - 7965 - 4 Dsy20170412A - 6481 - 4 Zdu20171114B - JJE - 3 Zdu20171020A - JJY - 4 Zdu20171031A - JJP - 3 Zdu20171121A - JJ6 - 4 Zdu20180403A - 11Z0 - 3 Dsy20180404A - 11Z8 - 3

I would like to be able to pull type of experiment from storage somehow using fish ID (not sure correct terminology) like "Dsy20160116A".

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karlcz commented 6 years ago

Did you guys ever talk about the access APIs used in the jupyter notebooks? I'm closing this with a few extra comments. Please re-open if you still need help...

At the model level, there is a boolean column on the Behavior table called Learned? which should be set to true or false for these runs. Using filters on this, it is easy to query for a list of just learners or just non-learners. I would expect this to remain null for the various control groups which experience a variant Behavior experiment (e.g. lacking CS and/or US) and those will also be associated with a different protocol.

In general, we don't directly associate a fish with a protocol. We associate it indirectly by linking individual observations (e.g. Image or Behavior records) with protocol steps (e.g. tpt1, tpt2, or behave) which are themselves children of a specific protocol. In general, I think an individual subject will only get associated with one protocol in this manner. But, the catalog model doesn't restrict this, so a messy longitudinal record could mix observations from several protocols...

Also, I don't think Bill's "stars" QA concept is captured in the catalog at present.