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Release notes

releases/0.100.0.rst releases/0.99.1.rst releases/0.99.0.rst releases/0.98.2.rst releases/0.98.1.rst releases/0.98.0.rst releases/0.97.1.rst releases/0.97.0.rst releases/0.96.1.rst releases/0.96.0.rst releases/0.95.1.rst releases/0.95.0.rst releases/0.94.0.rst releases/0.93.0.rst releases/0.92.0.rst releases/0.91.0.rst releases/0.90.1.rst releases/0.90.0.rst releases/0.13.0.rst releases/0.12.0.rst releases/0.11.0.rst releases/0.10.0.rst releases/0.9.9.rst releases/0.9.1.rst

Version 0.100.0

  • Several improvements and bug fixes for Windows users
  • Important refactoring of NWB extractors:
    • implemented direct backend implementation (to avoid using pynwb)
    • sped up streaming using remfile
    • added support for zarr backend
  • Removed joblib dependency in favor of ParallelProcessExecutor
  • Improved flexibility when running sorters in containers by adding several options for installing spikeinterface
  • Add Templates class to core, which handles unit templates and sparsity (#1982)
  • Added Zarr-backend to Sorting objects (sorting.save(folder="...", format="zarr")) (#2403)
  • Added SharedmemRecording for shared memory recordings (#2365)
  • Added machinery for moving/interpolating templates for generating hybrid recordings with drift (#2291)
  • Added new fast method for unit/spike/peak localization: grid_convolution (#2172)

Version 0.99.1

  • Minor release with some bug fixes

Version 0.99.0

  • Refactored core.generate module to create high-quality lazy ground-truth data
  • Added 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

Version 0.98.2

  • Minor release with some bug fixes

Version 0.98.1

  • Minor release with some bug fixes

Version 0.98.0

  • Implemented motion correction framework in SpikeInterface
  • Added "grid convolution" as localization method
  • Added amplitude_scaling implementation in postprocessing
  • Improved container support for docker and singularity
  • Improved implementation and performance of quality metrics module
  • Extensive additions to sortingcomponents` module (pipeline nodes, waveform denoising, sparsity)
  • _ind to _index in complex dtype representation for peak and spikes

Version 0.97.1

  • Minor release with some bug fixes and minor new features

Version 0.97.0

  • Implemented "sparse" waveforms in core and propagated to all modules:
    • Add waveform extractor save() function and Zarr backend
    • Dense waveforms can be saved as sparse with the save() function
    • Sparse waveforms can be extracted directly with sparse=True
  • Added IBL preprocessing tools for Neuropixels:
    • Bad channel detection
    • Channel interpolation
    • High-pass spatial filter
  • Add subfolder for sorter output ("output_folder/sorter_output") and sorting_info field to Sorting,
    so that "sorter_output" can be deleted without deleting metadata and sorting_info
  • Refactor Quality Metrics module:
    • Improve parameter handling
    • Unified naming and conventions
    • Add missing metrics: drift, amp medians, sliding_rp_violations
  • Extended Motion estimation and motion correction, which is now ready to use
  • Removed deprecated functions/modules:
    • toolkit module
    • symmetrize argument from compute_correlograms
    • localize_units from postprocessing
  • Major rewrite of the docs, with extensive module-specific documentation

Version 0.96.1

  • Bump up probeinterface version to 0.2.14 to fix bug in reading SpikeGLX contact locations

Version 0.96.0

  • Change setup.py to pyproject.toml
  • Enable loading waveform extractor without recording and with pre-existing sorting
  • Implement NpzFolder for saving Sorting object
  • Implement in-memory waveform extensions
  • Improve NEO event handling
  • Modify pyks for IBL version
  • Implement sparse PCA
  • Extend comparison to multi-segment sortings
  • Various improvements to widgets modules

Version 0.95.1

  • Widgets: Fix creation of 2D axes when figure is passed
  • Widgets: Add check for matplotlib backend when using ipywidgets

Version 0.95.0

  • Add BaseSnippets object to handle waveform cutouts
  • Sacrificed toolkit in favor of: preprocessing, postprocessing, qualitymetrics, and curation modules
  • Major refactoring widget module to allow for multiple backends
    • matplotlib
    • ipywidgets
    • sortingview
  • First implementations of (experimental) sortingcomponents-based sorters:
    • spykingcircus2
    • tridesclous2

Version 0.94.0

  • 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

Version 0.93.0

  • add WaveformExtractorExtension (PC, qualitymetrics, spike amplitudes) to automatically store and retrieve processed data waveforms folder
  • add singularity integration in run_sorter
  • add a link to the originating recording to the sorting object
  • new framework for collision benchmark
  • refactor comparison module and add TemplateComparison
  • add template_matching module (experimental)
  • add motion_correction module (experimental)

Version 0.92.0

  • many improvements in toolkit module
  • added spike unit localization
  • handle time vector in base recording

Version 0.91.0

  • Major improvements and bug-fixes.
  • Improvements for spikeinterface-gui.

Version 0.90.1

  • Minor release - bug fixes

Version 0.90.0

  • Major release:
    • many API modifications : no backward compatibility
    • contains all subpackages
    • get_traces() has transposed shape (time x channels)
    • handles multi segment
    • new WaveformExtractor object to handle waveforms computation
    • new Event object to handle epochs and events

LEGACY API

Version 0.13.0

  • Final release of version 0.1X - bug fixes

Version 0.12.0

  • Major update: API change for get_traces to enable return_scaled

Version 0.11.0

  • Bug fixes and improvements on efficiency

Version 0.10.0

  • Minor updates and bug fixes for biorXiv preprint

Version 0.9.9

  • Major updates and bug fixes to all packages - pre-release

Version 0.9.1

  • First SpikeInterface pre-release