Jadhav Lab Conversion Progress

[pauladkisson]

Jadhav Lab Conversion Progress

344/332 hrs

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

Conversion

Project 1: Behavior + Ephys (Jacob Olson)

• Epoch/Session Structure: Epoch #8

Behavior

• Behavior Interface: Behavior #4
• Video Interface: Adds Interfaces for SpikeGadgets and Video #2
• DLC Interface: DLC Interface #3

Ephys

• Fix SpikeGadgets Bug in Neo: Added support for missing channels in SpikeGadgets NeuralEnsemble/python-neo#1593
• SpikeGadgets Interface: Adds Interfaces for SpikeGadgets and Video #2
• LFPInterface: LFP #5
• Sorting Interface: Sorting #6

Temporal Alignment

• Align ephys, behavior, and video: Temporal alignment #9

Spyglass Compatibility

• Ensure spyglass v0.5.4 compatibility: Adding Spyglass Compatibility to the conversion #11
• Support for ndx-pose: Import pose edited LorenFrankLab/spyglass#1247
• Add support for latest changes to spyglass including DLC: Add support for dev version of Spyglass #13

Metadata

• Add/update metadata

Project 2: Behavior + Ephys (Edward Melendez & Ashutosh Shukla)

• Adapt Interfaces as necessary: Rivera and shukla #14
• Clean up code/Refactor to streamline different conversions: Refactor #15
• Convert all sessions: Convert all sessions #16
• README/Documentation: Documentation #17
• Behavior-only nwbfiles: DIO Events Require Ephys data to work LorenFrankLab/spyglass#1313 and Added support for DIO Events #19
• Invalid Intervals: Invalid intervals #18

Post-Conversion

• Setup Dandiset(s): #001343 and #001471
• Inspection/Validation: Added support for DIO Events #19
• Example Notebooks: Notebooks #20, Add example notebook for #001343 dandi/example-notebooks#116, Add example notebook for 001471 dandi/example-notebooks#117
• Final Meeting

Related Issues

ndx-franklab-novela

• optional shanksElectrode coordinates: ShanksElectrode coordinates should be optional LorenFrankLab/ndx-franklab-novela#13

Spyglass

• Imported Spikes: sgi.insert_sessions failing for ImportedSpikes LorenFrankLab/spyglass#1204
• Multiple Acquisition objects: Allow import of NWB file with multiple acquisition "Raw" data objects LorenFrankLab/spyglass#396
• Multiple Probes with the same probe_type: spyglass.data_import.insert_sessions omits a probe when 2 probes have the same probe_type LorenFrankLab/spyglass#1216
• Multi-row task table: Discussion: Why use many single-row tables for TaskEpoch? LorenFrankLab/spyglass#1221
• Cleaner VideoFile insertion: VideoFile should insert videos from ImageSeries instead of BehavioralEvents LorenFrankLab/spyglass#1224
• estimate_sampling_rate for irregular timestamps: estimate_sampling_rate fails for irregular timestamps when num_samples < 1e6 LorenFrankLab/spyglass#1240
• LFP ingestion in spyglass: Automatic insertion of pre-computed LFP data from NWB (i.e. ImportedLFP) LorenFrankLab/spyglass#1229
• Starting time and rate for PoseEstimationSeries LorenFrankLab/spyglass#1321
• How to represent "Unknown" time? LorenFrankLab/spyglass#1323
• Insert invalid_times to IntervalList LorenFrankLab/spyglass#1336

Neurosift

• Sub-selecting units/channels: Feature Request: Sub-selecting Units based on table properties and sub-selecting ElectricalSeries channels based on electrodes table properties flatironinstitute/neurosift#291
• PSTH for Behavioral Events: Feature Request: PSTH for BehavioralEvents flatironinstitute/neurosift#292
• PoseEstimationSeries: Feature Request: ndx-pose visualization flatironinstitute/neurosift#293

ndx-pose

• Device linkage: Pose estimation device linkage fails for ndx_franklab_novela.CameraDevice rly/ndx-pose#48