SFARI ARC - Kind Lab Conversion Progress

[alessandratrapani]

Fear Conditioning Dataset Conversion Progress

364/332

Pre-Conversion

• Repo Setup (Set up Conversion Project 1 #2, Set up Conversion Project 2 #3 )
• Initial Inspection and Notes: Delineation of Projects, Experiments and Data Streams
• Identify and request missing data/metadata/READMEs
• Acquire all data needed for conversion

Project 1: Behavior + Ephys

• Convert all sessions [Ephys] Convert all sessions #51

Behavior

Conversion with Spyglass compatibility

• Three-axis head-mounted accelerometer (OpenEphys) Ecephys spyglass conversion #5
• Video (".avi" or ".mkv" or ".ts") Ecephys spyglass conversion #5

Ingest in Spyglass

• Three-axis head-mounted accelerometer
• Video

External Stimuli

Conversion with Spyglass compatibility

• Behavioural paradigm triggers (CS/US) were programmed with Freeze Frame software (Actimetrics) (OpenEphys ".events") Ecephys spyglass conversion #5

Ingest in Spyglass

• Behavioural paradigm triggers (CS/US) Enhance behavioral events with detailed TTL channel information #24

Ephys

Conversion with Spyglass compatibility

• Local Field Potentials (LFP) (Intan/OpenEphys) Ecephys spyglass conversion #5
• Electro-EncephaloGram (EEG) (Intan/OpenEphys) Ecephys spyglass conversion #5

Ingest in Spyglass

• Local Field Potentials (LFP) Refactor add_electrical_series for LFP and EEG data handling #23
• Electro-EncephaloGram (EEG)

Temporal Alignment #50

Conversion with Spyglass compatibility

• TTL pulse --> all_channels.events (OpenEphys) Ecephys spyglass conversion #5

Ingest in Spyglass

• TTL pulse

Post-Conversion

• Setup Dandiset --> DANDI:001457
• Inspection/Validation
• README/Documentation [Ephys] Convert all sessions #51
• Example Notebooks Add tutorial notebooks #28

Project 2: Behavior only

7 different task only behavior

• Convert all sessions
• Spyglass ingestion (Add custom DataJoint table for annotated events and insertion function #46 )

1. Auditory Fear Conditioning #9 --> EMBER:000199

• Video (.ffii) (script to convert to avi)
• Freeze Behavior (.fft .ffdd --> FreezeFrame
• Behavior Analysis (.csv / .xls)

2. Object Location Memory #11 --> EMBER:000201

• Video (.ts or .mkv)
• Video Scores (.boris --> BORIS)

3. Object Recognition #10 --> EMBER:000202

• Video (.ts or .mkv)
• Video Scores (.boris)

4. Water Maze #12 --> EMBER:000205

• Video (.avi) -> needs timestamps where csv is not available
• Analysis with Actimetrix software (.wmpf and .csv) -> Information about the platform locations etc are contained in the CSV files. (.wmpf not needed)

5. Prey Capture #16 --> EMBER:000204

• Video (.ts files, .mp4 or .mkv)
• Ultrasonic Vocalisation (USV) (.wav)
• USV detection (.mat are they actually usable?)

6. Marble interaction #4 --> EMBER:000200

• Video (.ts or .mp4)

7. 1 Trial Social #22 --> EMBER:000203

• Video ()
• Ultrasonic Vocalisation (USV) (.wav)
• Video Scores (.boris)

Post-Conversion

• Setup Dandiset(s)
• Inspection/Validation
• README/Documentation
• Example Notebooks Add tutorial notebooks #28