Support for CZI images
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MaximLippeveld commented
To be able to handle CZI images we can load them using aicsimageio
. The CZI images contain 'scenes', each scene corresponds to a treatment. The scenes have dimensions MTCZXY equal to (56, 1, 6, 3, 1000, 1000). The user specifices which scene to process for each run through a command line argument or config entry.
The planes are stored as tiles. Each tile contains many cells which we want to identify through segmentation. The aicsimageio
provides access to image data as a Dask Array.