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One thing I noticed running over the hubmap data is that the labels from whole-slide imaging are not sequential, i.e. rather than [0, 1, 2, ... max_num_cells] it's [0, 459, 460, ... some_integer_much_larger_than_the_max_number_of_cells].
In principle this is still a valid mask, but it violates assumptions that folks have about label images. Fortunately the fix is as simple as skimage.segmentation.relabel_sequential; however, I'm making an issue as we need to add a test for this behavior. Coming up with that test will be where the real work lies!
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