Jadhav Lab Conversion Progress #1
Description
Jadhav Lab Conversion Progress
320/332 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