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wsireg v0.2.1

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@NHPatterson NHPatterson released this 14 Apr 19:43
· 248 commits to master since this release

This is a minor release with some improvements.

Update RegImage to support more image formats as well as make it easy to add new formats

  • add RegImage sub-classes for different file types
    • TiffFileRegImage (.scn, .ndpi,.tiff,.tif) : uses dask + zarr to do memory-efficient computation of necessary data for registration / transformation
    • CziRegImage (.czi) : Carl Zeiss image format, can perform read-time pre-processing like RGB -> greyscale or selection of individual channels to limit memory footprint
    • OmeTiffRegImage (.ome.tiff,ome.tif): uses TiffFile to read images and parses OME metadata to get interleaved RGB information
    • MergeRegImage (meta): used to transform multiple images' channels to a single OME-TIFF after registration if they output to the same size and data type (i.e. for cyclic IF)
    • 'NpRegImage' (np.ndarray): Supports adding a registration image from a numpy array
    • `SitkRegImage' (everything else): uses SimpleITK to read images as a last resort. Will read entire image into memory!

Add mask support and crop-to-mask support for registration

  • support masks for registration
    • Masks can be used in elastix to define pixels used in metric calculation
    • add ability to automatically crop images based on associated masks's bounding box (can be useful if image dimensions differ greatly)

Add class to manage transformations

  • use RegTransform class to manage transformations