v1.0.3

[cdgatenbee]

• Can specify which slide readers to use for each image by passing a dictionary to the reader_dict argument in Valis.register. The keys, value pairs are image filename and instantiated SlideReader to use to read that file. Valis will try to find an appropriate reader for any omitted files. Can be especially useful in cases where one needs different series for different images, as the series argument is set when the SlideReader is created.
• Each Slide is assigned aSlideReader, ensuring that the same series will always be read.
• Added traceback messages to critical try/except blocks to help with debugging.
• Micro-registration can now use multiple image processors, and so should be able to perform multi-modal registration
• Now possible to save the images as non-pyarmid WSI by setting pyramid=False when calling the various slide saving methods (requested in github issue 56).
• Tested the slide_io.CziJpgxrReader with more jpegxr compressed czi images, including 3 RGB (2 mosaic, 1 not mosaic), 1 multichannel non-RGB (mosaic), 1 single channel (mosaic). Related to github issue 76.
• Added checks to make sure all channel names are in the colormap, addressing github issues 78 and 86.
• Setting colormap=None to the various save functions will not add any color channels, and so the slide viewer's default colormaps will be used.
• Updated slide_io.get_slide_reader to give preference to reading images with libvips/openslide. Should be faster since image will not need to be constructed from tiles.
• JVM will only be initialized if bioformats is needed to read the image.
• Updated slide_io.VipsSlideReader to use the ome-types pacakge to extract metadata, instead of Bio-formats. Should avoid having to launch JVM unless Bio-formats is really needed.
• Added checks to ensure that channels in merged image are in the correct order when imgs_ordered=True, addressing the comment github issue 56.
• Added tests for images with minimal ome-xml (i.e. no channel names, units, etc...)
• Removed usage of imghdr, which is being deprecated
• Replaced joblib with pqdm. May resolve issue posted on image.sc
• Removed interpolation and numba packages as dependencies
• Updated ome-types' parser to "lxml"
• Merged github pull request 95

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This discussion was created from the release v1.0.3.