SpikeInterface 0.99.0 release notes¶
3rd November 2023
Main changes:
Refactored
core.generate
module to create high-quality lazy ground-truth dataAdded DeepInterpolation training, transfer, and inference to preprocessing
Added new quality_metrics (synchrony, firing_range, amplitude_cv)
Added new template metrics (num positive/negative peaks + multi-channel metrics: velocities, spread, exp. decay)
Important improvements to internal sorters (especially Spyking Circus 2)
Ported all widgets to “new” API and dismantled legacy widgets
Extensive clean-up of docstrings, code style, and documentation
core:
Handle edge frames in concatenated recordings (#1883)
Use spike_vector in count_num_spikes_per_unit (#1895)
Fix waveform extarctor crash with unfiltered wvf_extractor and sparsity (#1902)
Restore npzfolder.py file to load previously saved sorting objects (#1903)
Convert from samples<->times directly on BaseRecordings (#1921)
Move peak_pipeline into core and rename it as node_pipeline (#1941)
Implement SpikeRetriever pipeline source (#1944)
Refactor and improve generate.py (#1948, #1970, #2098)
Relax check_borders in InjectTemplatesRecording (#1988)
Speed up searchsorted calls across code-base (#2000)
Improve serialization concept : memory/json/pickle (#2027)
Check that main_ids are str or int (#2061)
Change some default parameters for better user experience (#2071)
Fix NoiseGeneratorRecording : “noise_level” in kwargs (#2084)
Add sparsity_temp_folder option to extract_waveforms (#2133)
Re-add relative_to to dump_to_pickle (#2129)
extractors:
Fix NWB streaming: do not convert to Path if ros3 or fsspec (#1875)
Add stream_name option to read_cbin_ibl (#1928)
Add RecordingExtractor for NeuroExplorer (#1965)
Fix Kilosort Phy reader docstrings (#2022)
Add ignore_timestamps_errors to OpenEphysLegacyRecordingExtractor (#2043)
CellExplorer: fix tests and deprecation (#2048)
Patch with scipy for remove_artefacts when mode is linear/cubic (#2072)
Fix grouping of OpenEphys NPIX extractors (#2102)
Fix open ephys probe loading and unify probeinterface import syntax (#2136)
preprocessing:
Deepinterpolation revived: training, transfer, and inference with more flexibility (#1804)
Patch silence_periods for mono-segment recordings (#1946)
Fix zero_channel_pad case when selected frames are outside of original data region (#1979)
Improve detect_bad_channels defaults and fixes (#2003)
Add an option to flip the order by depth (#2005)
Update a test expression to remove two logical short circuits in remove_artifacts (#2025)
Adjust eps for whitening in case of very small magnitude data (#2070)
sorters:
Add missing tic in ks*_master when skipping preprocessing (#1887)
Change the signature on kilosort’s delete intermediate files parameters (#1908)
Check if recording is JSON-serializable in run_sorter (#1932)
Spyking Circus 2 updates (#1943, #2074, #2080, #2086)
Tridesclous 2 updates (#2076, #2087, #2104)
Refactor sorter launcher. Deprecated run_sorters() and add run_sorter_jobs() (#1968)
Fixes Apptainer bug (#2053)
Use versioned kilosort options as default in skip_preprocessed_data (#2108)
Mountainsort5 version check fix (#2150)
postprocessing:
Amplitude scaling: add collisions handling (#1940)
Spike location with true spike channel (#1950)
Allow to postprocess on read-only waveform folders (#1957)
Refactor ISI calculation numpy and numba (#1958)
Extend and refactor waveform metrics, including multi-channel metrics (#1993)
Use default cutouts for peak-sign test (#2121)
Remove postprocessing template_tools (#2145)
qualitymetrics:
Fix bug in pca metrics warnings (#1874)
Implement syncrhrony metrics (#1951)
Additional amplitude CV and firing range metrics (#1981, #2054)
comparison:
Fix missing import pandas in comparison (#1872)
Refactoring of GroundTruthStudy (#1983)
Save/load comparison objects with pickle (#2013)
Improved GTStudy and related widgets (#2128)
Optimize make_match_count_matrix with numba (#2114)
curation:
Allow MergeUnitsSorting to handle tuple inputs (#1995)
Fix: Correct unit ID matching in sortingview curation (#2037)
exporters:
Fix bug in export_to_phy with sparsity (#1904)
Allow relative path for export_to_phy (#2041)
Change phy exporter to not save template_ind in the case of dense waveform_extractor (#2148)
widgets:
Port legacy widgets to new API (#2016, #2068, #2115, #2124)
For connoisseur only: add a simple “ephyviewer” backend plot_traces() (#2024)
Improve ipywidgets backend (#2035, #2079, #2091)
Improved GTStudy and related widgets (#2128)
Add assert error in the case of unichannel data for sortingview backend + minor clarifications (#2149)
sortingcomponents:
Implement proof of concept merge_clusters/split_clusters (#1996)
Add SVD convolutions to template matching (#2045)
docs:
Several typo and display fixes, mainly thanks to @zm711 (#1866, #1898, #1990, #1992, #1936, #1953, #2015, #2019, #2036, #2057, #2100, #2103, #2130)
Update installation Tips (#1962)
Add “how to” section on how to load matlab data (#2018, #2047)
Add link to latest pypi version docs in readme (#2060)
Improve assert messages (#2078, #2109, #2119)
Unify ‘defaults’ and use of quotations across docstrings (#2134)
Add Docstring section to development docs (#2138)
ci / packaging / tests:
Fix the [full] install for Macs (#1955)
Change np.in1d to np.isin as the former will be deprecated (#2002)
Fix folder for installation test build (#2004)
Extend common postprocessing tests to spikes at borders (#2014)
Add SPIKEINTERFACE_DEV_PATH to aws gpu tests (#2088)
Fix git-annex installation (#2097)
Add actual test for check_your_install (#2112)
Add quality_metrics specific module requirements to pyproject.toml (#2135)