Release notes

Version 0.100.4

  • Minor release with extended compression capability for Zarr

Version 0.100.3

  • Minor release with bug fixes for Zarr compressor and NWB in container

Version 0.100.2

  • Minor release with fix for running Kilosort4 with GPU support in container

Version 0.100.1

  • Minor release with some bug fixes and Kilosort4 support

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 (”…”, 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 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


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