Cell segmentation and representation with shape priors

Abstract

Cell segmentation is a fundamental problem of computational biology, for which convolutional neural networks yield the best results nowadays. This field is expanding rapidly, and in the recent years, shape-constrained segmentation models emerged as strong competitors to traditional, pixel-based segmentation methods for instance segmentation. These methods predict the parameters of the underlying shape model, so choosing the right shape representation is critical for the success of the segmentation. In this study, we introduce two new representation-based deep learning segmentation methods after a quantitative comparison of the most important shape descriptors in the literature. Our networks are based on Fourier coefficients and statistical shape models, both of which have proven to be reliable tools for cell shape modelling. Our results indicate that the methods are competitive alternatives to the most widely used baseline deep learning algorithms, especially when the number of parameters for the underlying shape model are low or the cells to be segmented have irregular morphologies.

Keywords

• Shape representation
• Deep learning
• Fourier descriptors
• Statistical shape models
• Cell segmentation