Overview of the segmentation algorithm. The main steps of the algorithm are illustrated here on a small portion of a slice through the middle of an embryo. Note that the actual images are three-dimensional and comprise a whole embryo. The DNA image is the input Sytox channel. A shell mask defines the region that contains all the information of interest for the segmentation algorithm: the blastoderm nuclei with a small part of the cytoplasm. The DNA mask distinguishes the nuclei from the background (cytoplasm, yolk, and so on). The seeds image contains the local maxima of the smoothed DNA, a Gaussian filtered version of DNA image. Surface normals are computed for each seed from the shell, and used to prune the seeds. The image nuclei is the nuclear segmentation mask, dividing the DNA mask into individual nuclei. The dotted arrow going back to the pruned seeds represents the addition of seeds according to the results obtained in nuclei. The apical cytoplasm and basal cytoplasm mark the cytoplasmic regions for each nucleus estimated using a tessellation.