Dan Lab Conversion Progress

[pauladkisson]

Dan Lab Conversion Progress

174/250 hrs

Data/Metadata Sharing

• Example session w/ TDT FP data
• Example session w/ TDT EEG/EMG data
• Example session w/ Video data
• Example session w/ "pTra_con"-style optogenetics
• Example session w/ "opto"-style optogenetics
• Example metadata info.mat file
• 2 Multi-session datasets for protocol 1
• Example session w/ DLC data
• DLC config.yaml
• Example session w/ Behavioral labels (labels.mat) and summary (beh_summary.csv)
• Example session w/ EEG and EMG stored in .mat files
• Multi-session dataset for protocol 2
• Histology
• Multi-session dataset for protocol 3
• Lots of metadata
• Ephys-Video Temporal Alignment data for protocol 2

Conversion (Lindsay Huang)

Protocol 1: Fiber Photometry + EEG + EMG + Video + Ogen

• Temporal Alignment
• Convert all sessions: Convert all sessions #17

Fiber Photometry

• Fiber Photometry Interface: Fiber photometry #3
• Add stub_test option to TDTFiberPhotometryInterface: Added stub_test option to TDTFiberPhotometryInterface neuroconv#1242
• Add both FP fibers: Updated Fiber Photometry to include both fibers #7
• Add FP metadata

Video

• Video Interface: Video #2
• Update video on neuroconv: Split VideoInterface into ExternalVideoInterface and InternalVideoInterface neuroconv#1251
• Update Video to use new interface: Switched to new ExternalVideoInterface #11
• Add video metadata

EEG + EMG

• Ephys Interface: Lfp #4
• Split into eeg vs emg: Split LFP into EEG and EMG electrode groups #9
• Add ephys metadata

Ogen

• Ogen Interface w/o Extension: OptogeneticInterface #8
• Ogen Extension:
  • Optional viruses rly/ndx-optogenetics#5
  • Link OptogeneticEpochsTable to rows of OpticalFiberLocationsTable rly/ndx-optogenetics#6
  • Discussion: Should ndx-optogenetics use OpticalFiber and ExcitationSource from ndx-ophys-devices? rly/ndx-optogenetics#7
• Ogen Interface w/ Extension: Opto #12

Protocol 2: Video + Behavior + PoseEstimation + EEG + EMG

• Temporal Alignment
• Convert all sessions: Convert all sessions #17

Behavior

• Behavior Interface: Behavior #14

PoseEstimation

• DLCInterface: DLC Interface and separate protocols #13

Video

• Video Interface: DLC Interface and separate protocols #13

EEG + EMG

• .mat based Ephys interface: mat-based EEG + EMG #15

Protocol 3: 24hr EEG/EMG + Behavior

• Temporal Alignment
• Convert all sessions

Behavior

• Behavior Interface

EEG + EMG

• .mat based Ephys interface

Histology

• Histology Interface

Post-Conversion

• Setup Dandiset(s)
• Inspection/Validation
• README/Documentation
• Example Notebooks
• Update CN Website
• Final Meeting

Related Issues

Neuroconv

• add_electrical_series_to_nwbfile's write_scaled doesn't do anything if True neuroconv#1266

NWB Best Practices

• Best Practice for EMG data? NeurodataWithoutBorders/nwbinspector#579

ndx-pose

• Use ImageSeries for original and labeled videos rly/ndx-pose#13