SpikeInterface 0.95.0 release notes

2nd September 2022

Main changes:

• Add BaseSnippets object to handle waveform cutouts (https://github.com/SpikeInterface/spikeinterface/pull/764)

• Sacrificed toolkit in favor of: preprocessing, postprocessing, qualitymetrics, and curation modules (https://github.com/SpikeInterface/spikeinterface/pull/745)

• Major refactoring widget module to allow for multiple backends (https://github.com/SpikeInterface/spikeinterface/pull/686 / https://github.com/SpikeInterface/spikeinterface/pull/786 / ) * matplotlib * ipywidgets * sortingview

• First implementations of (experimental) sortingcomponents-based sorters: * spykingcircus2 (https://github.com/SpikeInterface/spikeinterface/pull/787) * tridesclous2 (https://github.com/SpikeInterface/spikeinterface/pull/800)

core:

• Add ZARR storage_options argument to enable cloud read/write (https://github.com/SpikeInterface/spikeinterface/pull/622)

• Add seed for sampling waveforms (https://github.com/SpikeInterface/spikeinterface/pull/629)

• Allow for unconnected contacts when setting probe (https://github.com/SpikeInterface/spikeinterface/pull/646)

• Refactor nested recursive functions (https://github.com/SpikeInterface/spikeinterface/pull/651 / https://github.com/SpikeInterface/spikeinterface/pull/774)

• Switch to packaging (https://github.com/SpikeInterface/spikeinterface/pull/697)

• Add BinaryFolderRecording and is_binary_compatible() (https://github.com/SpikeInterface/spikeinterface/pull/726)

• Fixed SharedMemory buffer (https://github.com/SpikeInterface/spikeinterface/pull/741)

• Improve handling of unitless NEO extractors (https://github.com/SpikeInterface/spikeinterface/pull/758)

• Add mp_context arg to control multiprocessing (https://github.com/SpikeInterface/spikeinterface/pull/781)

• Option to automatically cast unsigned dtypes in get_traces (https://github.com/SpikeInterface/spikeinterface/pull/798)

• Add mode=”memory” for WaveformExtractor (https://github.com/SpikeInterface/spikeinterface/pull/832)

• Patch memory leak when saving to Zarr (https://github.com/SpikeInterface/spikeinterface/pull/915)

• Add return_scaled in write_to_h5 format (https://github.com/SpikeInterface/spikeinterface/pull/908)

• Improved NEO wrapper to handle multi-blocks and return number of blocks and stream info (https://github.com/SpikeInterface/spikeinterface/pull/909)

• Update OpenEphys and SpikeGLX for NEO and ProbeInterface releases (https://github.com/SpikeInterface/spikeinterface/pull/916)

extractors:

• Fix 1D kilosort/phy spiketrains (https://github.com/SpikeInterface/spikeinterface/pull/617)

• Propagate NEO annotations to SI objects (https://github.com/SpikeInterface/spikeinterface/pull/627)

• Add AlphaOmega support (https://github.com/SpikeInterface/spikeinterface/pull/637)

• Improve BIDS reader (https://github.com/SpikeInterface/spikeinterface/pull/647)

• Add ros3` support for NWB (https://github.com/SpikeInterface/spikeinterface/pull/658)

• Fix neo kwargs propagation (https://github.com/SpikeInterface/spikeinterface/pull/723)

• Load ADC sample shifts for Open Ephys and SpikeGLX (Neuropixels) (https://github.com/SpikeInterface/spikeinterface/pull/734 / https://github.com/SpikeInterface/spikeinterface/pull/759)

• Load gain for MEArec (https://github.com/SpikeInterface/spikeinterface/pull/791)

• Added functions to get extractors from name (https://github.com/SpikeInterface/spikeinterface/pull/835)

• Update nwb recording extractor to use offsets (https://github.com/SpikeInterface/spikeinterface/pull/846)

• Add EDFRecordingExtractor, NeuralynxSortingExtractor, BlackrockSortngExtractor (https://github.com/SpikeInterface/spikeinterface/pull/853 / https://github.com/SpikeInterface/spikeinterface/pull/854 / https://github.com/SpikeInterface/spikeinterface/pull/856)

• Fix IBL cbin kwargs (https://github.com/SpikeInterface/spikeinterface/pull/873)

• Add snippets extractors: MClust (https://github.com/SpikeInterface/spikeinterface/pull/879) - WaveClus (https://github.com/SpikeInterface/spikeinterface/pull/764)

• Fix Phy reading when unit groups are excluded (https://github.com/SpikeInterface/spikeinterface/pull/876)

sorters:

• Allow to propagate local SI installation to docker/singularity container (https://github.com/SpikeInterface/spikeinterface/pull/630)

• Refactor MATLAB-based sorters to allow compiled versions (https://github.com/SpikeInterface/spikeinterface/pull/631 / https://github.com/SpikeInterface/spikeinterface/pull/660 / https://github.com/SpikeInterface/spikeinterface/pull/649 / https://github.com/SpikeInterface/spikeinterface/pull/684)

• Fix docker mechanisms for Windows (https://github.com/SpikeInterface/spikeinterface/pull/635)

• Remove unused mdaio from IronClust (https://github.com/SpikeInterface/spikeinterface/pull/638)

• Add wave_length param to kilosort (https://github.com/SpikeInterface/spikeinterface/pull/655)

• Better handling of GPU requirements (https://github.com/SpikeInterface/spikeinterface/pull/674)

• Add default container map (https://github.com/SpikeInterface/spikeinterface/pull/685)

• Add extra_requirements mechanism to install required packages in container (https://github.com/SpikeInterface/spikeinterface/pull/689)

• Unify handling of job_kwargs across sorters (https://github.com/SpikeInterface/spikeinterface/pull/706)

• Optional motion correction for KS2.5 and KS3 (https://github.com/SpikeInterface/spikeinterface/pull/709)

• Dump npz sorting in container (https://github.com/SpikeInterface/spikeinterface/pull/779)

• Add tmpdir parameter to MS4 (https://github.com/SpikeInterface/spikeinterface/pull/827)

• Add SLURM launcher (https://github.com/SpikeInterface/spikeinterface/pull/828)

• Add WaveClus from snippets implementation (https://github.com/SpikeInterface/spikeinterface/pull/764)

• Extend docker map to HerdingSpikes and Combinato (https://github.com/SpikeInterface/spikeinterface/pull/891 / https://github.com/SpikeInterface/spikeinterface/pull/889)

• Fixes to pykilosort (https://github.com/SpikeInterface/spikeinterface/pull/890)

preprocessing:

• Allow artifact removal of single sample when ms_before=ms_after=None (https://github.com/SpikeInterface/spikeinterface/pull/618)

• Add operator to CMR kwargs (https://github.com/SpikeInterface/spikeinterface/pull/634/files)

• Add DeepInterpolationRecording (https://github.com/SpikeInterface/spikeinterface/pull/661)

• Add zscore preprocessing (https://github.com/SpikeInterface/spikeinterface/pull/679)

• Enable specification of dtype for whitening (https://github.com/SpikeInterface/spikeinterface/pull/881)

postprocessing:

• Fix template metrics return values (https://github.com/SpikeInterface/spikeinterface/pull/620)

• Add sparsity option for template metrics (https://github.com/SpikeInterface/spikeinterface/pull/629)

• Added SpikeLocationsCalculator as WaveformExtension (https://github.com/SpikeInterface/spikeinterface/pull/735)

• Improve efficiency and verbosity of PCA (https://github.com/SpikeInterface/spikeinterface/pull/739)

• Add ISI histograms (https://github.com/SpikeInterface/spikeinterface/pull/760)

• Refactor ISI histograms, CrossCorrelograms, TemplateSimilarity, and UnitLocations extensions (https://github.com/SpikeInterface/spikeinterface/pull/778)

• Fix fancy indexing for arrays (https://github.com/SpikeInterface/spikeinterface/pull/816)

qualitymetrics:

• Improved tests (https://github.com/SpikeInterface/spikeinterface/pull/692)

• Add sparsity to quality metrics computation (https://github.com/SpikeInterface/spikeinterface/pull/739)

curation:

• Add CurationSortingExtractor class (https://github.com/SpikeInterface/spikeinterface/pull/612)

• Add deduplication of spike trains (https://github.com/SpikeInterface/spikeinterface/pull/776 / https://github.com/SpikeInterface/spikeinterface/pull/817)

comparison:

• Fix multicomparison duplicate removal (https://github.com/SpikeInterface/spikeinterface/pull/620)

• Add option to remove sorters folder in GTStudy (https://github.com/SpikeInterface/spikeinterface/pull/629)

• Better internal handling of comparison objects in multicomparison (https://github.com/SpikeInterface/spikeinterface/pull/732)

widgets:

• Improved similarity widget (https://github.com/SpikeInterface/spikeinterface/pull/665)

• Allow selection of waveforms to plot (https://github.com/SpikeInterface/spikeinterface/pull/672/files)

• Add Tiled plot (https://github.com/SpikeInterface/spikeinterface/pull/693 / https://github.com/SpikeInterface/spikeinterface/pull/821)

• Refactor multiple widgets (https://github.com/SpikeInterface/spikeinterface/pull/762 / https://github.com/SpikeInterface/spikeinterface/pull/820)

• Multi-layer timeseries (https://github.com/SpikeInterface/spikeinterface/pull/783)

• Add sorting_summary widget for sortingview (https://github.com/SpikeInterface/spikeinterface/pull/795)

• Fix generation of docstrings for plot_ functions (https://github.com/SpikeInterface/spikeinterface/pull/920)

• Unify generation of 2d axes in MPL (https://github.com/SpikeInterface/spikeinterface/pull/921)

sortingcomponents:

• Component-specific benchmarks (https://github.com/SpikeInterface/spikeinterface/pull/667 / https://github.com/SpikeInterface/spikeinterface/pull/678 / https://github.com/SpikeInterface/spikeinterface/pull/839)

• Restructure matching module (https://github.com/SpikeInterface/spikeinterface/pull/668)

• Refactor motion correction (https://github.com/SpikeInterface/spikeinterface/pull/669)

• Add numba isocut implementation (https://github.com/SpikeInterface/spikeinterface/pull/688)

• Add nearest neighbor NN triaging (https://github.com/SpikeInterface/spikeinterface/pull/694/files)

• Add compute features from peaks (https://github.com/SpikeInterface/spikeinterface/pull/754)

• Implement “peak pipeline” (https://github.com/SpikeInterface/spikeinterface/pull/845)

docs:

• Documentation updates for quality_metrics (https://github.com/SpikeInterface/spikeinterface/pull/666)

• Automatic generation of function from classes (https://github.com/SpikeInterface/spikeinterface/pull/673)

• Add intersphinx for neo readers (https://github.com/SpikeInterface/spikeinterface/pull/677)

• Improve API documentation (https://github.com/SpikeInterface/spikeinterface/pull/691)

• Improve documentation of containerized sorters (https://github.com/SpikeInterface/spikeinterface/pull/765 / https://github.com/SpikeInterface/spikeinterface/pull/777)

• Expose classes in the API docs (https://github.com/SpikeInterface/spikeinterface/pull/863)

CI:

• Add NWB ros3 test

• Add code coverage (https://github.com/SpikeInterface/spikeinterface/pull/675)

• Create automatic issue when a MATLAB file is changes – might require docker image update (https://github.com/SpikeInterface/spikeinterface/pull/756)