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Non-binary embedding of a 3D stack of a neutrophil cell. (a-c) are the 5th, 8th, and 11th slices. The estimated embedding function is in the form of a level set of a grey-scale volume. This representation facilitates detecting or filling-in of holes. Topology is evaluated starting from inside (levels with high value) and progressing towards the outer layers (low values) to find the largest thresholded binary volume with spherical topology.
