Add eye tracking data to Neuropixels NWB files

AllenInstitute / AllenSDK

code for reading and processing Allen Institute for Brain Science data

https://allensdk.readthedocs.io/en/latest/

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Add eye tracking data to Neuropixels NWB files #1392

Closed wbwakeman closed 4 years ago

wbwakeman commented 4 years ago

Since allensdk.brain_observatory.ecephys.write_nwb was first created, we have stabilized eye tracking and caught up on processing. Need to make sure this data is being incorporated into the NWB file.

wbwakeman commented 4 years ago

Investigate how much additional work this would really be, given that eye tracking is available in cache.

njmei commented 4 years ago

[x] Try generating nwbfile with on updated pynwb feature branch
[x] Check that AllenSDK nwb api can indeed access eye tracking / eye gaze data from nwbfile
[ ] ~Contact Josh with sample notebooks accessing eye tracking and see if any other changes are requested~ (leaving this for another ticket which involves checking and fixing all ecephys notebooks)

EDIT: See #1552 for new ticket covering last checkbox

njmei commented 4 years ago

Eye tracking data can be accessed from newly created nwbfiles:

Screenshot from 2020-05-04 16-24-27

rly commented 4 years ago

Would it be possible to take a look at one of these NWB files? Are you using an extension to store the eye-tracking data in a structured way?

njmei commented 4 years ago

@rly I can put together a sample NWB file once I get the majority of other NWB related work done.

Eye-tracking data is being stored in either DynamicTables for the raw ellipse fits for pupil, corneal reflection, and eyelid. Gaze mapped coordinates (using ellipse fits to map where gaze should be on a screen) are saved as TimeSeries.