Model-based segmentation and quantification of fluorescent bacteria in 3D microscopy live cell images

We introduce a new model-based approach for segmenting and quantifying fluorescent bacteria in 3D microscopy live cell images. The approach is based on a new 3D superellipsoidal parametric intensity model, which is directly fitted to the image intensities within 3D regions-of-interest. Based on the fitting results, we can directly compute the total amount of intensity (fluorescence) of each cell. In addition, we introduce a method for automatic initialization of the model parameters, and we propose a method for simultaneously fitting clustered cells by using a superposition of 3D superellipsoids for model fitting. We demonstrate the applicability of our approach based on 3D synthetic and real 3D microscopy images.