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Upcoming (v0.5.11)

Features

Fixes

Improvements

  • Use pyproject.toml for project metadata and installation requirements #382

v0.5.10 (November 6th, 2024)

Features

  • Added a seed to dummy generators #361
  • Added depth_slice for VolumetricImagingExtractors PR #363

Fixes

  • Added specific error message for single-frame scanimage data PR #360
  • Fixed bug with ScanImage's parse_metadata so that it works properly when hStackManager is disabled PR #373
  • Add support for background components in FrameSliceSegmentationExtractor PR #378

Improvements

  • Removed unnecessary import checks for scipy, h5py, and zarr PR #364
  • Improved the error message for the set_timestamps method in the ImagingExtractor classPR #377
  • Renamed MiniscopeImagingExtractor toMiniscopeMultiRecordingImagingExtractor classPR #374

v0.5.9

Deprecations

  • Remove support for Python 3.8: PR #325

Features

  • Add InscopixImagingExtractor: #276
  • Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: PR #317
  • Added API documentation: #337
  • Optimized get_streams for BrukerTiffSinglePlaneImagingExtractor by introducing a static function get_available_channels which uses lazy parsing of the XML to fetch the available channels: #344

Fixes

  • Remove unnecessary scipy import error handling: #315
  • Fixed the typing returned by the InscopixImagingExtractor.get_dtype method: #326
  • Detect Changelog Updates was moved to its own dedicated workflow to avoid daily testing failures: #336
  • Fixed the Daily testing workflows by passing along the appropriate secrets: #340
  • Change the criteria of determining if Bruker data is volumetric #342
  • Fixes a bug that assumes the channel name is is on the tiff file for BrukerTiffSinglePlaneImagingExtractor #343
  • Including packaging explicitly in minimal requirements #347
  • Updated requirements to include cv2 and update dev testing locations for neuroconv: #357

Improvements

  • The Suite2PSegmentationExtractor now produces an error when a required sub-file is missin: #330
  • Added _image_mask initialization in BaseSegmentationExtractor; combined abstractmethods into top of file: #327
  • Optimize parsing of xml with lxml library for Burker extractors: #346
  • Protect sima and dill export #351
  • Improve error message when TiffImagingExtractor is not able to form memmap #353
  • Updated Check Docstrings workflow to use new github action: #354

Testing

  • Updated testing workflows to include python 3.12, m1/intel macos, and dev tests to check neuroconv: PR #317
  • Added daily testing workflow and fixed bug with python 3.12 by upgrading scanimage-tiff-reader version: PR #321
  • Remove wheel from requirements and move CI dependencies to test requirements PR #348
  • Use Spikeinterface instead of Spikeextractors for toy_example PR #349

v0.5.8

Fixes

  • The triggering workflow name for update version was incorrectly set to auto-publish (the name of the yaml file). It has been renamed to Upload Package to PyPI (the name field of the workflow): PR #304.

  • Fixed bug with automatic changelog test that was causing it to fail for daily tests: PR #310

  • Updated zenodo to get a DOI on each release: No PR

v0.5.7

Features

  • Add support to get background components: add get_background_ids(), get_background_image_masks(), get_background_pixel_masks() to SegmentationExtractor. PR #291

  • Add distinction for raw roi response and denoised roi response in CaimanSegmentationExtractor: PR #291

  • Bug fix for the CaimanSegmentationExtractor: correctly extract temporal and spatial background components PR #291

  • Added automatic version update workflow file that will run after publishing a new release to pypi: PR #290

  • Added ScanImageTiffSinglePlaneMultiFileImagingExtractor and ScanImageTiffMultiPlaneMultiFileImagingExtractor: PR #297

  • Added automatic changelog checking in the test workflow: PR #302

Fixes

  • Improved xml parsing with Bruker PR #267

  • Fixed a bug with ScanImageTiffSinglePlaneImagingExtractor in which frames_per_slice would be set to _num_frames: PR #294

v0.5.6

Features

  • Added support for red channel (anatomical) ROIs from suite2p in Suite2pSegmentationExtractor: PR #270

  • Added support for RoiGroup metadata in the extract_extra_metadata function for ScanImageTiff files: PR #272

  • Updated documentation and Readme PRs: #283 #282 #280

v0.5.5

Features

  • Updated Suite2pSegmentationExtractor to support multi channel and multi plane data. PR #242

Fixes

  • Fixed MicroManagerTiffImagingExtractor private extractor's dtype to not override the parent's dtype. PR #257
  • Fixed override of channel_name in Suite2pSegmentationExtractor. PR #263

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

  • Added support for incomplete file ingestion for the Suite2pSegmentationExtractor. PR #227

  • Bug fix for the CaimanSegmentationExtractor: Change reshaping from 'C' to 'F' (Fortran). PR #227

  • Bug fix for the CaimanSegmentationExtractor: Added importing of self._image_correlation and changed how self._image_mean to import the background component image. PR #227

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.