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Transgenic zebrafish expressing fluorescent proteins in specific tissues or organs are promising models for studies of normal developmental processes, or perturbations of these. However, for widespread use, reliable quantification of the observed effects is necessary. Therefore, accurate and automatic analysis of images obtained by fluorescent microscopy and depicting zebrafish embryos becomes crucial. In this paper, a segmentation approach for such images is proposed. The segmentation is achieved by fitting a species-specific 2D atlas to the zebrafish data depicted in the images. Experiments performed in a set of 50 images have provided promising results.