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CHANGELOG.md

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Upcoming

v0.5.4

Features

  • Added volumetric and multi-channel support for Bruker format. PR #230

v0.5.3

Features

  • Added support for Miniscope AVI files with the MiniscopeImagingExtractor. PR #225

v0.5.2

Features

  • Added support for MicroManager TIFF files with the MicroManagerTiffImagingExtractor. PR #222

  • Added support for Bruker TIFF files with the BrukerTiffImagingExtractor. PR #220

v0.5.1

Features

  • Added a has_time_vector function for ImagingExtractors and SegmentationExtractors, similar to the SpikeInterface API for detecting if timestamps have been set. PR #216

Fixes

  • Fixed two issues with the SubFrameSegementation class: (i) attempting to set the private attribute _image_masks even when this was not present in the parent, and (ii) not calling the parent function for get_pixel_masks and instead using the base method even in cases where this had been overridden by the parent. PR #215

v0.5.0

Back-compatability break

  • The orientation of traces in all SegmentationExtractors has been standardized to have time (frames) as the first axis, and ROIs as the final axis. PR #200

Features

  • Add support for newer versions of EXTRACT output files. PR #170 The ExtractSegmentationExtractor class is now abstract and redirects to the newer or older extractor depending on the version of the file. PR #170
  • The ExtractSegmentationExtractor.write_segmentation method has now been deprecated. PR #170

Improvements

  • Add frame_to_time to SegmentationExtractor, get_roi_ids is now a class method. PR #187
  • Add set_times to SegmentationExtractor. PR #188
  • Updated the test for segmentation images to check all images for the given segmentation extractors. PR #190
  • Refactored the NwbSegmentationExtractor to be more flexible with segmentation images and keep up with the change in catalystneuro/neuoroconv#41 of trace names. PR #191
  • Implemented a more efficient case of the base ImagingExtractor.get_frames through get_video when the indices are contiguous. PR #195
  • Removed max_frame check on MultiImagingExtractor.get_video() to adhere to upper-bound slicing semantics. PR #195
  • Improved the MultiImagingExtractor.get_video() to no longer rely on get_frames. PR #195
  • Added dtype consistency check across MultiImaging components as well as a direct override method. PR #195
  • Added the FrameSliceSegmentationExtractor class and corresponding Segmentation.frame_slice(...) method. PR #201
  • Changed the output_struct_name argument to optional in ExtractSegmentationExtractor. to allow more flexible usage for the user and better error message when it cannot be found in the file. For consistency, output_struct_name argument has been also added to the legacy extractor. The orientation of segmentation images are transposed for consistency in image orientation (height x width). PR #210
  • Relaxed rounding of ImagingExtractor.frame_to_time(...) and SegmentationExtractor.frame_to_time(...) to be more consistent with SpikeInterface. PR #212

Fixes

  • Fixed the reference to the proper mov_field in Hdf5ImagingExtractor. PR #195
  • Updated the name of the ROICentroids column for the NwbSegmentationExtractor to be up-to-date with NeuroConv v0.2.0 write_segmentation. PR #208
  • Updated the trace orientation for the NwbSegmentationExtractor. PR #208

v0.4.18

Improvements

  • get_video is now an abstract method in ImagingExtractor PR #180

Features

  • Add dummy segmentation extractor PR #176

Testing

  • Added unittests to the get_frames method from ImagingExtractors to assert that they are consistent with numpy indexing behavior. PR #154
  • Tests for spikeinterface like-behavior for the get_video funtiction PR #181

v0.4.17

Depreceations

  • Suite2P argument has become folder_path instead of file_path, file_path deprecation scheduled for august or later.

Documentation

  • Improved docstrings across many extractors.

Features

  • Adds MultiImagingExtractor for combining multiple imaging extractors.
  • Adds ScanImageTiffExtractor for reading .tiff files output from ScanImage
  • Adds NumpyImagingExtractor for extracting raw video data as memmaps.
  • Added frame slicing capabilities for imaging extractors.

Testing

  • Added checks and debugs that all sampling frequencies returns are floats
  • Round trip testing working for all extractors that have a working write method.