Dombeck Lab Conversion

[weiglszonja]

Dombeck Lab Conversion Progress

The SOW includes #1 and #4 but there is another fiber photometry experiment (ongoing data collection) that we learnt about (see #5).

Fiber photometry (Azcorra 2023)

• Collect initial notes : Azcorra2023 - Fiber photometry conversion notes #1 , 2P conversion notes #4
• Collect missing data (see Notes)
• Add extractor and interface for PicoScope signals (Add traces from PicoScope #2)
• Add extractor and interface for raw fiber photometry (binned files, ready for review PR: Add fiber photometry #7)
• Add interface for processed photometry data
  • note about data6.mat Azcorra2023 - Fiber photometry conversion notes #1 (comment)
  • draft PR: Add processed fiber photometry #10
• Run conversion for all sessions
• Run nwbinspector and collect issues
• Fix any inconsistencies that are in the files, collect issues
• Create demo notebook Add tutorial notebook #30
• Create landing page for fiber photometry dataset on DANDI (confirm public upload)
• Upload sessions and update dandiset metadata

Two photon experiment (Ongoing data collection)

• Add multifile scan image interface to NeuroConv Add interface for single and multi-file ScanImage TIFF files neuroconv#809
• Add two photon imaging Add two photon imaging #8
• Add Suite2p segmentation output Add suite2p #11
• Add motion corrected imaging data Add motion correction #12
• Add camera recordings (.tif files) and add pose estimation Add behavior for two photon #13
• Add time alignment Add behavior for two photon #13
• Collect subject metadata
• Convert example session
• Schedule mid-way meeting after fiber photometry is concluded and two photon pipeline is ready

New fiber photometry experiment (Ongoing data collection)

• Add interface for optogenetic stimuli: Add optogenetic stimulation #38
• If time left add fiber photometry data from AxoBits (not in SOW) - in progress (Add processed fiber photometry #40)

Collect Source data

Fiber photometry (finished and ongoing project)

• optogenetic stimuli: this is included in the new fiber photometry experiment (details in New Fiber photometry data notes #5)
• raw video camera recordings: this is included in the new fiber photometry experiment (details in New Fiber photometry data notes #5)
• Mouse metadata (age, strain, date since injection)
• synch signals: the synchronisation between the camera and data acquisition (this is also in New Fiber photometry data notes #5)

Two photon experiment (ongoing project)

• raw multichannel 2p imaging data (ScanImage)
• motion correction
• Suite2p segmentation
• treadmill velocity, including signal from a break to control friction
• signals from lick tube (reward times, licking times) - NO lick signals only locomotion experiment
• DLC config.yaml