Fig. 1

Image segmentation challenges. a Reconstructed cross-section of a SPIM light sheet microscopy volume of the ascidian P. mammillata showing an artifact in which as many as five nuclei appear connected. This makes it difficult for existing nuclei detection methods to properly segment. b Weak signal in the membrane channel in lower z slices of a confocal microscopy image. c Inconsistent signal strength in the cell wall channel of a z slice through a confocal microscopy image of Arabidopsis thaliana (image courtesy Elliot Meyerowitz Lab, Division of Biology, California Institute of Technology). d Cells with interrupted membrane which share cytoplasm, as in this example of the Caenorhabditis elegans gonad cells [32]. Watershed segmentation methods will have difficulty segmenting such structures due to leakage. e Sperm cells appear in the nuclei channel resulting in false positives for a nuclei detector [32]. f Dividing P. mammillata cell SPIM images that show up as large nuclei