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@pauladkisson pauladkisson released this 07 Jul 21:23
· 97 commits to main since this release
v0.6.1
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Features

  • Added native timestamp support with automatic fallback hierarchy: get_native_timestamps() abstract method and get_timestamps() concrete method to all imaging and segmentation extractors. The get_timestamps() method follows priority order: cached times → native timestamps → inferred from sampling frequency. This enables automatic native timestamp usage when available (e.g., ScanImage TIFF files) while maintaining backward compatibility. PR #465
  • Added property management methods to SegmentationExtractor: set_property(), get_property(), and get_property_keys() for storing and retrieving custom ROI properties PR #467
  • Added MinianSegmentationExtractor for reading and extracting metadata and segmentation data from Minian output files.PR #368

Fixes

  • Fixed a bug in CaimanSegmentationExtractor where empty components of the segmentation traces will throw an error
    PR #452

Deprecations And Removals

  • Remove deprecated arguments combined and plane_no from Suite2pSegmentationExtractor PR #457
  • check_imaging_equal and check_segmentation_equal no longer compare the number of channels in an extractor as that attribute has been deprecated PR #470
  • exclude_channel_comparison in check_imaging_equal is deprecated and will be removed in or after January 2026. This parameter is no longer needed as extractors do not have multiple channels. PR #470
  • The num_frames parameter in generate_dummy_imaging_extractor and generate_dummy_segmentation_extractor is now deprecated and will be removed on or after January 2026. Use the new num_samples parameter instead. num_samples is now keyword-only and will become positional-only in a future release. PR #470
  • The sample_indices_to_time() method in both ImagingExtractor and SegmentationExtractor is deprecated and will be removed on or after January 2026. Use get_timestamps() instead. PR #448
    Remove deprecated arguments combined and plane_no from Suite2pSegmentationExtractor PR #457

Improvements

  • Updated GitHub Actions workflows to use cross-OS cache sharing for multi-OS testing data, reducing redundant downloads and improving CI efficiency. Added reusable data loading action pattern similar to neuroconv. PR #459
  • Improved writing to NWB documentation to point out users to neuroconv PR #468
  • Add comprehensive test suite for CaimanSegmentationExtractor covering basic properties, ROI masks, traces, accepted/rejected lists, and different CaImAn dataset formats PR #464
  • Add isort and remove unused imports to pre-commit PR #471
  • Updated tests for CaimanSegmentationExtractor to cover all stub files, and enhanced the extractor to return quality metrics (r_values, SNR_comp, cnn_preds). PR #466
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