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0.94.0.rst

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SpikeInterface 0.94.0 release notes

15th April 2022

Main change:

  • Refactor WaveformExtractor with waveform_tools.
  • Implement Zarr backend for save()
  • Read IBL compressed files.
  • Phase shift (destripe) preprocessor
  • Test are run partially : faster GH actions
  • Many improvement in sorting compnents: template matching, select_peaks, motion_estimation, motion_correction

core:

  • Fix typo in SplitSegmentSorting init
  • Added NumpySorting.from_peaks()
  • Refactor WaveformExtractor with waveform_tools.
  • Fix bug "too many open files" for the new waveforme extractor.
  • Add function to remove empty units
  • Remove loose version in favor of packaging
  • Add chunk_duration concept for jobs
  • Implement Zarr backend for save()
  • Add split recording class and function
  • Add Recording.remove_channels()
  • Add save sorting to memory

extractors:

  • Reintroduce spikeglx test files
  • Add NeuroscopeSortingExtractor
  • New neo extractors
  • Add more neualynx versions for testing
  • Modify nwb recorder extractor for loading channel name property as channel_ids when available
  • Support 3d positions (rel_z) in NWB
  • Read openephys probe from probeinterface
  • Fix "KSLabel" extraction in phykilosortextractor
  • Bug fix on waveclus sorting extractor
  • Read IBL compressed files

sorters:

  • Refactor run_sorters/run_sorter_by_group to better handle folders and key dtypes

toolkit:

  • Phase shift (destripe) preprocessor
  • Fix typo in isi violation
  • Addresses batch size bug #565, and also resolves open file warnings
  • Add nan to d_prime for single unit case
  • Handle computing of nearest neighbor metrics for units with few spikes

comparison:

  • Fix multisortingcomparison spiketrains

widgets:

  • Add presence plot
  • Add with_channel_ids for several widgets that use plot_probe
  • Add optional distinctipy

export:

  • Fix mismatch between phy and si unit ids

sortingcomponents:

  • Improvements to template matching
  • Start sparse clustering
  • Improvements to select_peak()
  • Improvements to motion_estimation()
  • Improvements to motion_correction()
doc:
  • Documentation updates for quality_metrics
  • Try install SI from conda env and skip pip
  • Improve documentation for sorting components

CI:

  • Refactor tests
  • Partial tests
  • Fix herdingspikes version for tests