Comments (6)
Did first TODO, second one will take more work because quite a lot changed
https://spikeinterface.readthedocs.io/en/latest/releases/0.90.0.html#release0-90-0
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To be clear, the current install instruction conda env create -f environment.yml
does not create a working environment because spikeinterface==0.90 gets installed, which means packages like spikesorters and spiketoolkit are not installed.
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Thanks, will look into this
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Seems like quite a bit of stuff that we need is not implemented yet in spikeinterface 0.90 (e.g. writing recording and sorting to nwb files, computing some of the metrics like noise overlap etc) so will hold off on migrating completely to it for now to preserve functionality
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should be addressed by pr #118. there are some improvements to still be made, e.g. writing recording and sorting directly to nwb by spikeinterface function calls. will create a new issue for these. other than that i think we have all the features we need, including the quality metrics.
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Related Issues (20)
- Multiprocess populate when make function uses parallelization HOT 3
- merged_sorting_extractor not found HOT 3
- Peripheral tables cause issues: deletes, field name uniqueness, etc.
- `01_Insert_Data.ipynb` assumes lab member name will be inserted via nwb HOT 1
- Inserting nwb file without trodes tracking leads to no entries in RawPosition HOT 1
- DLC Centroid populate error with spatial_series HOT 5
- Remove unused tables HOT 1
- Merge duplicate funcs HOT 3
- generate merge suggestions for all sorted clusters HOT 5
- Insufficient varchar length for `AnalysisNwbfileLog.table`
- 'TableChain' object has no attribute 'join' HOT 1
- `dj_graph` prompt to spawn missing classes
- Implement `spikesorting.v1.MetricCuration.get_waveforms`
- `IntegrityError` or foreign key error when inserting into table HOT 1
- Automated pytests of position pipeline in GitHub actions
- Length mismatch for upsampled data in `fill_nan`
- argument error in notebook
- AnalysisNwbfileLog requires insert/delete privileges for read-only users HOT 1
- Insert session from Dandi
- Resolve case of shared file use in multiple Dandisets
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