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v0.5.13

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@pauladkisson pauladkisson released this 12 May 19:25
· 132 commits to main since this release
v0.5.13
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Features

  • Added ScanImageImagingExtractor for simplifying reading ScanImage data PR #412
  • Added volumetric imaging support with is_volumetric flag, get_frame_shape, get_num_planes, and get_volume_shape methods PR #418
  • Added support for multiple samples per slice to ScanImageIMagingExtractor PR # 417
  • Added support for flyback frames to ScanImageImagingExtractor PR #419
  • Added InscopixSegmentationExtractor for reading .isxd segmentation files #407
  • Add plane_index to ScanImageImagingExtractor to obtain a planar extractor across a plane PR #424
  • Add testing to timestamp extraction on ScanImageImagingExtractor PR #426
  • Add paths as string support to ScanImageImagingExtractor PR #427
  • Add informative error for old ScanImage files with ScanImageImagingExtractor PR #427
  • Add the option to read interleaved data in ScanImageImagingExtractor PR #428
  • Add detection of missing files in a sequence and excess file for ScanImageImagingExtractor file find heuristic PR #429

Fixes

  • Fixed get_series method in MemmapImagingExtractor to preserve channel dimension PR #416
  • Fix memory estimation for volumetric imaging extractors in their _repr_ PR #422

Deprecations And Removals

  • The get_video(start_frame, end_frame) method is deprecated and will be removed in or after September 2025. Use get_series(start_sample, end_sample) instead for consistent naming with get_num_samples. PR #416
  • Python 3.9 is no longer supported PR #423
  • The time_to_frame() method is deprecated and will be removed in or after October 2025. Use time_to_sample_indices() instead for consistent terminology between planar and volumetric data. PR #430
  • The frame_to_time() method is deprecated and will be removed in or after October 2025. Use sample_indices_to_time() instead for consistent terminology between planar and volumetric data. PR #430
  • The frame_slice() method is deprecated and will be removed in or after October 2025. Use slice_samples() instead for consistent terminology between planar and volumetric data. PR #430
  • The FrameSliceImagingExtractor class is deprecated and will be removed in or after October 2025. Use SampleSlicedImagingExtractor instead for consistent terminology between planar and volumetric data.
    PR #430
  • Long deprecated ScanImageTiffImagingExtractor is removed. For ScanImage legacy data use ScanImageLegacyImagingExtractor PR #431
  • Deprecated ScanImageTiffMultiPlaneMultiFileImagingExtractor, ScanImageTiffSinglePlaneMultiFileImagingExtractor, ScanImageTiffMultiPlaneImagingExtractor, and ScanImageTiffSinglePlaneImagingExtractor classes. These will be removed on or after October 2025. Use ScanImageImagingExtractor instead. PR #432

Improvements

  • Improved criteria for determining if a ScanImage dataset is volumetric by checking both SI.hStackManager.enable and SI.hStackManager.numSlices > 1PR #425
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