Zaki 2024 Conversion (Cai lab)

[alessandratrapani]

This is to organize the conversion.

TO-DO:

• Schedule initial meeting to ask for external resources and general info on experimental sessions
• Add conversion notes Add conversion notes #2
• Add Miniscope support for this conversion (Add miniscope interface #8)
• Add preprocessed imaging data (Minian) (Complete conversion pipeline: code refactoring #10)
• Add segmentation (Minian) calcium events (Minian) Add Minian Segmention Interface #7 Add Minian segmentation extractor roiextractors#368 add Minian data interface neuroconv#1107
• Add EMG signals (.edf) Add EEG, MEG, Temperature and Activity Interfaces #3
• Add EEG signals (.edf) Add EEG, MEG, Temperature and Activity Interfaces #3
• Add EEG-related events, e.g, sleeping phase (.csv) Add sleep behavior interface #6
• Add behavioral events: freezing behavior (EZTrack) Add Frezing Behavior Interface #4
• Add motion series (EZTrack) Add motion series from eztrack #9
• Add raw behavioral video Complete conversion pipeline: code refactoring #10
• Write a conversion script for a condition day (Neutral or Aversion) (Add conversion script for conditioning sessions #11)
• Write a conversion script for an offline day. (Add offline sessions to the conversion script #12)
• Slice EDF data for each offline session. (EDF time slicing #15)
• Add shock times (Add shock stimuli interface and metadata #17)
• Convert the week-long eeg/emg data Add week long session #18
  • Include the cell registration output Add cell registration #19
  • Include epochs of the smaller session in the week-long file Add epochs to week long session #20
• Double check synchronization of the data streams. Time alignment #23
  • eztrack motion series
  • miniscope/minian imaging data
  • Timing of miniscope: see that this comment is addressed. Sort out whether frame rate from metadata or video should be used (see comment) (Add imaging timestamps using new conversion option always_write_timestamps #16)
• Add subject/session metadata (Add shock stimuli interface and metadata #17, Add subject metadata and generate session description for each session #22)
• Check the metadata for imaging interfaces. Are we missing something? excitation lambda? plane geometry? location?
• Run validation over both condition and offline days using nwbinspector
• Modify the documentation in the readme so it releases the latest working version and file structure. (Add demo notebook #13)
• Create run conversion tutorial. add run conversion tutorial #25
• Create demos notebook and DANDI landing page Add demo notebook #13
• Upload to DANDI (WIP)
• Schedule final meeting