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Merge pull request #81 from lguerard/issues/34
Update changelog
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CHANGELOG.md

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* New `imcflibs.imagej.bdv` submodule, providing BigDataViewer related
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functions:
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* New classes:
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* `ProcessingOptions` to store all options on how to process the dataset.
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* `DefinitionOptions` to store all options on how to define the dataset.
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* `imcflibs.imagej.bdv.ProcessingOptions` to store all options on how to process the dataset.
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* `imcflibs.imagej.bdv.DefinitionOptions` to store all options on how to define the dataset.
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* `imcflibs.imagej.bdv.check_processing_input` to sanitize and clarify the
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acitt input selection.
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* `imcflibs.imagej.bdv.get_processing_settings` to generate the strings needed
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Dataset" using the "Manual Loader" option.
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* `imcflibs.imagej.bdv.resave_as_h5` to resave the dataset in H5 to make it
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compatible with BigDataViewer/BigStitcher.
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* `imcflibs.imagej.bdv.flip_axes` tocall BigStitcher's "Flip Axes" command.
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* `imcflibs.imagej.bdv.flip_axes` to call BigStitcher's "Flip Axes" command.
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* `imcflibs.imagej.bdv.phase_correlation_pairwise_shifts_calculation` to
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calculate pairwise shifts using Phase Correlation.
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* `imcflibs.imagej.bdv.filter_pairwise_shifts` for filtering pairwise shifts
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* New `imcflibs.imagej.trackmate` submodule to provide helper functions to
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interface with Trackmate:
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* Multiple functions to set up Trackmate settings with different detectors,
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such as `cellpose`, `StarDist` or a `log detector`.
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such as `imcflibs.imagej.trackmate.cellpose_detector`, `imcflibs.imagej.trackmate.stardist_detector` or a `imcflibs.imagej.trackmate.log_detector`.
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* `imcflibs.imagej.trackmate.spot_filtering` to create settings to filter
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detected spots based on optional thresholds for quality, area, circularity &
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intensity.
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* `imcflibs.imagej.projections.project_stack` to project along a defined axis
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using the given projection type.
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### Changed
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* `imcflibs.pathtools.listdir_matching` now has an additional optional boolean
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parameter `regex` to request the parameter `suffix` being interpreted as a
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regular expression for filtering.
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* `imcflibs.imagej.misc.calculate_mean_and_stdv` to allow for rounding the results.
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## 1.4.0
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### Added

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