Generating session metadata from the GUI

[XX-Yin]

• Behavior session metadata

  • Which fields should go to the behavior session metadata? https://github.com/AllenNeuralDynamics/dynamic-foraging-task/issues/303#issuecomment-2062196234
  • Existing fields in the behavior GUI
    • [x] experimenter_full_name
    • [x] session_start_time
    • [x] session_end_time
    • [x] subject_id
    • [x] session_type
    • [x] animal_weight_post
    • [x] water calibration
    • [x] laser calibration
    • [x] reward_consumed_total
    • [x] reward_consumed_unit
    • [x] adding training stage
  • Missing fields from the current behavior json?
    • [x] Ephys recording information
    • [x] Ephys probe configuration
    • [x] Probe target
    • [x] Ephys probe manipulator coordinates
    • [x] Stick microscopes configuration
    • [x] Camera start/stop time
    • [x] iacuc_protocol
    • [x] protocol_id
    • [x] rig_id (rig metadata)
    • [x] data_streams
    • [x] behavior
    • [x] video
    • [x] ephys
    • [x] reward_delivery
    • [x] stimulus
    • [x] optogenetics
    • [x] auditory cue
    • [x] box name
  • To do:
  • [x] Generating metadata directly at the end of each session.
  • [x] Generating metadata from input json files.
  • [x] Handle edge cases.
  • [x] Generating metadata for old sessions with some fields missing.

• Ephys session metadata

• Related repo:

  • https://github.com/AllenNeuralDynamics/CTLUT-metadata-gen/tree/main/src/CTLUT_metadata_gen
  • https://github.com/AllenNeuralDynamics/aind-metadata-mapper
  • https://github.com/AllenNeuralDynamics/aind-data-schema

• Related discussion:

  • https://github.com/AllenNeuralDynamics/aind-behavior-blog/issues/68
  • https://github.com/AllenNeuralDynamics/dynamic-foraging-task/issues/303#issuecomment-2062196234

• Online app:

  • https://metadata-entry.allenneuraldynamics.org/

• Questions/Issues

  • [x] What is Modality.TRAINED_BEHAVIOR?
    • old version
  • [x] What is the stimulus device name for TRAINED_BEHAVIOR?
    • old version
  • [x] Distance between the two lick spouts?
    • [x] We should define the lick spout reference position.
  • [x] adding "Face side left" and "Face side right" to devices/CameraTarget
    • [x] Saskia will make changes.
  • [x] OptoStimulation needs changes there are other protocols and the stimulation period is also flexible. It is better to extract information from NWB. Make fields in the OptoStimulation optional)
    • [x] Go to stimulus epoch
  • [x] mouse_platform_name and active_mouse_platform are only necessary for behavior data stream.
  • [x] Is data description necessary?
  • [x] Combine different data streams
    • Separate different streams are much more flexible.
  • [x] Missing Laser in STIMULUS_DEVICES (rig.py)
  • [x] Missing Fujinon in LENS_MANUFACTURERS (organizations.py) https://github.com/AllenNeuralDynamics/aind-data-schema-models/issues/4
  • [x] Missing organization Midwest Optical Systems. Inc. in Organization (organizations.py). https://github.com/AllenNeuralDynamics/aind-data-schema-models/issues/5
  • [x] https://github.com/AllenNeuralDynamics/aind-data-schema/issues/920
  • [ ] https://github.com/AllenNeuralDynamics/aind-data-schema/issues/926
  • [ ] https://github.com/AllenNeuralDynamics/aind-data-schema/issues/927

[alexpiet]

@XX-Yin Have these remaining tasks been resolved? If not can you either resolve them or assign someone?

[XX-Yin]

@alexpiet most of these issues have been solved. Some issues don't have a short-term solution.

[alexpiet]

@alexpiet most of these issues have been solved. Some issues don't have a short-term solution.

Can you mark off the ones that have been resolved, and make a separate issue for each remaining one?