Learnable snake r-cnn for instance-level biomedical image segmentation

Precisely knowing each instance's position and extents is a critical first step in many biological applications. State-of-the-art techniques rely either on deep learning models designed to predict segmentation masks on each Region of Interest (RoI) or on classic active contour methods. The former struggles to precisely delineating boundaries and tends to output masks at low resolutions when the cells/nuclei are very irregular while the latter often needs good initialization and manual setting of parameters, thus limiting their usefulness. To bridge this gap, we introduce Snake R-CNN, a new level of the learnable active contour model that predict boundary on each RoI in a sequent way. To do so, for each RoI, we reformulate the contour deformation task in terms of a hidden state evolution problem and update the evolution process using energy minimization. We learn snake parameterizations per instance in an end-to-end manner, and demonstrate its effectiveness for contour inferences of various cell/nucleus types where consistently higher performances were obtained for comparison against state-of-the-arts.