RAW DATA structure on aind/scratch
📂###### (6 digit mouse ID)/
┣ 🖼️vasculature_map.tif
┣ 🖼️vasculature_map_annotated.tif* (constantly updated)
┣ 📦######_YYYY-MM-DD_HH-MM-SS (for stacks, Session ID by Mouse ID and datetime)/ <- this is the folder that will become a data asset on CodeOcean
┃ ┣ 📜rig.json
┃ ┣ 📜session.json
┃ ┣ 📜subject.json (created during upload to S3, not on VAST)
┃ ┣ 📜data_description.json (created during upload to S3, not on VAST)
┃ ┣ 📜metadata.nd.json (created during upload to S3, not on VAST)
┃ ┣ 📜procedures.json (created during upload to S3, not on VAST)
┃ ┣ 📜processing.json (created during upload to S3, not on VAST)
┃ ┃
┃ ┗ 📂slap2/
┃ ┣ 🖼️vasculature_map_annotated.tif (copied from * upon upload to VAST)
┃ ┣ 🖼️session_vasculature_1p.tif
┃ ┗ 📂static_data
┃ ┣ 📜structure_YYYYMMDD_HHMMSS_DMD#.meta
┃ ┣ 💾structure_YYYYMMDD_HHMMSS_DMD#.dat
┃ ┣ 🖼️structure_YYYYMMDD_HHMMSS_DMD#.tif
┃ ┗ 🖼️structure_YYYYMMDD_HHMMSS_DMD#-REFERENCE.tif
┃
┣ 📦######_YYYY-MM-DD_HH-MM-SS (for experiments, Session ID by Mouse ID and datetime)/ <- this is the folder that will become a data asset on CodeOcean
┃ ┣ 📜rig.json
┃ ┣ 📜session.json
┃ ┣ 📜subject.json (created during upload to S3, not on VAST)
┃ ┣ 📜data_description.json (created during upload to S3, not on VAST)
┃ ┣ 📜metadata.nd.json (created during upload to S3, not on VAST)
┃ ┣ 📜procedures.json (created during upload to S3, not on VAST)
┃ ┣ 📜processing.json (created during upload to S3, not on VAST)
┃ ┃
┃ ┣ 📂behavior/
┃ ┃ ┣ 📂VCO1_Behavior.harp
┃ ┃ ┃ ┣ 💾Behavior_#.bin (# is the register number)
┃ ┃ ┃ ┗ 📜device.yml
┃ ┃ ┗ 💾<any stim file name>.csv (useful behavior csv files)
┃ ┃
┃ ┣ 📂behavior-videos/
┃ ┃ ┣ 📂BodyCamera
┃ ┃ ┃ ┣ 📹video.mp4 (video.avi for now)
┃ ┃ ┃ ┗ 📜metadata.csv (metadata.json for now)
┃ ┃ ┣ 📂FaceCamera
┃ ┃ ┃ ┣ 📹video.mp4 (video.avi for now)
┃ ┃ ┃ ┗ 📜metadata.csv (metadata.json for now)
┃ ┃ ┗ 📂EyeCamera
┃ ┃ ┣ 📹video.mp4 (video.avi for now)
┃ ┃ ┗ 📜metadata.csv (metadata.json for now)
┃ ┃
┃ ┗ 📂slap2/
┃ ┣ 🖼️vasculature_map_annotated.tif (copied from * upon upload to VAST)
┃ ┣ 🖼️session_vasculature_1p.tif
┃ ┗ 📂dynamic_data
┃ ┣ 📜acquisition_YYYYMMDD_HHMMSS_DMD#.meta
┃ ┣ 💾acquisition_YYYYMMDD_HHMMSS_DMD#-TRIAL######(-CYCLE######).dat
┃ ┣ 🖼️acquisition_YYYYMMDD_HHMMSS_DMD#-TRIAL######(-CYCLE######).tif (only sometimes there, depending on SLAP2 mode)
┃ ┣ ...
┃ ┗ 📂reference_stack
┃ ┣ 📜refStack_YYYYMMDD_HHMMSS_DMD#(_CONFIG#).meta
┃ ┣ 💾refStack_YYYYMMDD_HHMMSS_DMD#(_CONFIG#).dat
┃ ┣ 🖼️refStack_YYYYMMDD_HHMMSS_DMD#(_CONFIG#).tif
┃ ┗ 🖼️refStack_YYYYMMDD_HHMMSS_DMD#(_CONFIG#)-REFERENCE.tif
┃
┣ 📦######_YYYY-MM-DD_HH-MM-SS_processed_YYYY-MM-DD_HH-MM-SS (first datetime corresponds to the original session data asset, second datetime corresponds to time of starting processing)
┃ ┣ 📜rig.json (carried over from raw data)
┃ ┣ 📜session.json (carried over from raw data)
┃ ┣ 📜subject.json (carried over from raw data)
┃ ┣ 📜data_description.json (carried over from raw data)
┃ ┣ 📜metadata.nd.json (carried over from raw data)
┃ ┣ 📜procedures.json (carried over from raw data)
┃ ┣ 📜processing.json (updated based on processing pipeline that was run)
┃ ┣ 📜qc.json (updated based on processing pipeline that was run)
┃ ┃
┃ ┣ 📜trialTable.mat
┃ ┃
┃ ┣ 📂motion_correction
┃ ┃ ┣ 📜E#T#DMD#_ALIGNMENTDATA.mat
┃ ┃ ┣ 🖼️E#T#DMD#_REGISTERED_DOWNSAMPLED-##Hz.tif
┃ ┃ ┗ ...
┃ ┃
┃ ┣ 📂source_extraction
┃ ┃ ┣ 📜ExperimentSummary.mat
┃ ┃ ┗ 📜ExperimentSummary.h5
┃ ┃
┃ ┗ 📂qc
┃ ┗ ...TBD...
┃
┗ 📦######_YYYY-MM-DD_HH-MM-SS_<processed modality>_YYYY-MM-DD_HH-MM-SS (first datetime corresponds to the original session data asset, second datetime corresponds to time of starting processing)
┣ 📜rig.json (carried over from raw data)
┣ 📜session.json (carried over from raw data)
┣ 📜subject.json (carried over from raw data)
┣ 📜data_description.json (carried over from raw data)
┣ 📜metadata.nd.json (carried over from raw data)
┣ 📜procedures.json (carried over from raw data)
┣ 📜processing.json (updated based on processing pipeline that was run)
┣ 📜qc.json (updated based on processing pipeline that was run)
┃
┣ 📂<processing step, i.e. annotations>
┃ ┗ ...
┃
┗ 📂qc