NWB files tables in the files need to be reorganized to follow some standardized convention

[alexpiet]

• nwb.stimulus should contain:
  • go Cue (currently only in trials)
  • rewards (currently in acquisitions, and only has time of rewards, not size)
    • data should contain the reward volume, instead of "1" which is the current value
• scratch['metadata'] should have all the information in the aind-metadata session.json, right?
• nwb.experimenter is none
• nwb.session_description is the string "Test File"
• nwb.lab is none
• nwb.notes is none (we have notes in the metadata)
• nwb.protocol is none
• nwb.surgery is none
• nwb.virus is none

[hanhou]

scratch['metadata'] should have all the information in the aind-metadata session.json, right?

Actually the opposite is true. Scratch is my temporary way of storing meta data, so we should remove it and make sure that all information in the scratach exists in the json metadata files.

[Ahad-Allen]

• nwb.stimulus should contain:

  • go Cue (currently only in trials)

  • rewards (currently in acquisitions, and only has time of rewards, not size)

    • data should contain the reward volume, instead of "1" which is the current value

  • scratch['metadata'] should have all the information in the aind-metadata session.json, right?

  • nwb.experimenter is none

  • nwb.session_description is the string "Test File"

  • nwb.lab is none

  • nwb.notes is none (we have notes in the metadata)

  • nwb.protocol is none

  • nwb.surgery is none

  • nwb.virus is none

Most of this makes sense to update! We can pull a lot of the missing metadata from the json files. The scratch section should be removed, as Han pointed out. I'm a little confused on the changes you'd like to do to the stimulus. Are you suggesting we add the Stim table with reward times and go Cues in it(I am not sure what a go Cue is, but that is probably just my ignorance on experimental design here)? That shouldn't be too large of a change, if so!

[alexpiet]

Yes, we should add a stimulus table with reward times (water delivery, currently in acquisition), and go cue (sound played to the mouse, currently only in the trials table)

[Ahad-Allen]

@rachelstephlee here's the metadata objects we should be adding

[rachelstephlee]

where was the session_description set? I can't re-set it. NWB gives me an error that the attribute is already set.

[rachelstephlee]

@rachelstephlee will followup with @Ahad-Allen on this.

[Ahad-Allen]

I believe @rachelstephlee already did some work on adding most of this metadata, and I have some code that should move where the gocues are present. We still need to add reward volume and remove scratch. I can work on these now

[Ahad-Allen]

Good news, the reward volume size is already in the trials table as reward_size_left and reward_size_right. I added the gocues in the feat-4 branch. I'll push a pr now

[Ahad-Allen]

PR: https://github.com/AllenNeuralDynamics/NWB-Packaging-FiberPhotometry-Base-Capsule/pull/21

[alexpiet]

Updated specs: nwb.acquisitions['left_reward_delivery_time'].data should contain reward volume

These fields should be grabbed from the aind metadata files

• [x] nwb.experimenter is none
• [ ] nwb.session_description is the string "Test File"
  • Should we copy the data_description.json here?
• [x] nwb.lab is none
• [ ] nwb.notes is none (we have notes in the metadata)
• [x] nwb.protocol is none
• [x] nwb.surgery is none
• [ ] nwb.virus is none
• [ ] entries of acquistions should not exist if there is no data - FIP falling/rising time, and optogenetics

[alexpiet]

https://github.com/AllenNeuralDynamics/NWB-Packaging-FiberPhotometry-Base-Capsule/pull/16 adds nwb.surgery, nwb.Experimenter, nwb.protocol, and nwb.lab

[alexpiet]

Need to define an NWB specification here

[jeromelecoq]

Assigning to Alex to finish document. @Ahad-Allen can handle once done.

[alexpiet]

This NWB extension is for adding AIND metadata to NWB files https://github.com/AllenNeuralDynamics/ndx-aind-metadata