Optree: A Learning-Based Adaptive Watershed Algorithm for Neuron Segmentation

Mustafa Gökhan Uzunbas, Chao Chen, Dimitris N. Metaxas

Abstract: We present a new algorithm for automatic and interactive segmentation of neuron structures from electron microscopy (EM) images. Our method selects a collection of nodes from the watershed merging tree as the proposed segmentation. This is achieved by building a conditional random field (CRF) whose underlying graph is the merging tree. The maximum a posteriori (MAP) prediction of the CRF is the output segmentation. Our algorithm outperforms state-of-the-art methods. Both the inference and the training are very efficient as the graph is tree-structured. Furthermore, we develop an interactive segmentation framework which selects uncertain regions for a user to proofread. The uncertainty is measured by the marginals of the graphical model. Based on user corrections, our framework modifies the merging tree and thus improves the segmentation globally.