IBL mesoscope Conversion Project Progress

[alessandratrapani]

IBL mesoscope Conversion Project Progress

Pre-Conversion

• Repo Setup
• Initial Inspection and Notes: Delineation of Projects, Experiments and Data Streams
• Identify and request missing data/metadata/READMEs
• Acquire all data needed for conversion
  dual plane sessions:
  c13eb6d3-09f5-49f7-bd89-26fce25ff65f
  1e558505-7d94-4851-83ef-edb2844ee805
  6f12a581-2203-4cd3-97b4-cd9cd78b440e
  ##IBL data types datasheet:
  https://docs.google.com/spreadsheets/u/1/d/1ieLXRPLLSgUKcLvFkrqizfZl5HjdfE6bQ2KLBCRmjQo/edit?usp=drive_web&ouid=107692576857324699678

Conversion

Active Behavior

Raw

• Raw behavioral video [REFACTORING] Raw Conversion Pipeline #10
• Natural video replay intervals

Processed

• Lick times Add processed behavior interfaces #7
• Wheel data Add processed behavior interfaces #7
• Pose estimation Add processed behavior interfaces #7
• Roi motion energy Add processed behavior interfaces #7
• Brainwide Map trials Add processed behavior interfaces #7

Passive behavior

Raw

• Raw behavioral video [REFACTORING] Raw Conversion Pipeline #10

Raw calcium imaging

• ScanImage raw output (on a separate nwbfile) [low priority] Add raw mesoscope data interface and extractor #3

Motion corrected series

• Suite2p motion registration output (single channel, multiplane/multiFOV) Add processed imaging data #4

Processed calcium imaging

• Suite2p ROIs detection (mapped on ONE API) Add processed imaging data #4
• ROICat output (cross sessions registration) --> global ids column

Anatomical localization

https://github.com/int-brain-lab/ibllib/blob/6d3b0897a28b96311b0e7878ca5f0abf38355ba3/ibllib/pipes/mesoscope_tasks.py#L1228C8-L1229C43
using ndx-anatomical-localization

• ROIs anatomical localization Add anatomical localization interface #5
• FOV anatomical loc Add anatomical localization interface #5 (Mean Image as Reference --> Proposal: Add AnatomicalCoordinatesImage Neurodata Type ndx-anatomical-localization#8)

Temporal Alignment

• Synch signals reader add DAQ sync signals #12

Subject and Session metadata

• Subject metadata
• Session metadata

Post-Conversion

Tutorials / Documentation

• README/Documentation

Raw

• Example Notebooks Add raw mesoscope data interface and extractor #3

Processed

• Example Notebooks Add processed imaging data #4

Behavior

• Example Notebooks Add processed behavior interfaces #7

DANDI

• Setup Dandiset
• Inspection/Validation
• Upload all sessions
• Final Meeting