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A variety of algorithms (Eliceiri et al., 2012; Jug et al., 2014; Yu et al., 2009) are available for segmentation of nuclei, including: watershed, iterative voting methods, level set approach based on gradient flow and flexible contour model. However the implementation of these algorithms to segment Light Sheet Fluorescent Microscopy (LSFM) data is not straightforward, due to complex installation procedures, or difficulty in tuning the parameters for individual biological samples. Moreover, a good segmentation result relies not only on an efficient segmentation algorithm but also on a sequence of steps preparing the image so that the segmentation algorithm can perform efficiently. Therefore, putting all these steps together requires a systematic design of the pipeline and the interface.
(Gole., 2016) OpenSegSPIM: a user-friendly segmentation tool for SPIM data. Bioinformatics.