3D segmentation and quantification of mouse embryonic stem cells in fluorescence microscopy images

We present an automatic approach for 3D segmentation of mouse embryonic stem cell nuclei based on level set active contours. Due to the specific properties of these cells, standard methods for cell nucleus segmentation and splitting of cell clusters cannot be applied. Our segmentation approach combines information from two different channels which represent the nuclear region and the nuclear membrane. Moreover, we perform segmentation of gene loci within two other channels which enables single cell quantification of gene distances.