RESEARCH ARTICLE A Context-Aware Delayed Agglomeration Framework for Electron Microscopy Segmentation

Electron Microscopy (EM) image (or volume) segmentation has become significantly impor-tant in recent years as an instrument for connectomics. This paper proposes a novel ag-glomerative framework for EM segmentation. In particular, given an over-segmented image or volume, we propose a novel framework for accurately clustering regions of the same neu-ron. Unlike existing agglomerative methods, the proposed context-aware algorithm divides superpixels (over-segmented regions) of different biological entities into different subsets and agglomerates them separately. In addition, this paper describes a “delayed ” scheme for agglomerative clustering that postpones some of the merge decisions, pertaining to newly formed bodies, in order to generate a more confident boundary prediction. We report significant improvements attained by the proposed approach in segmentation accuracy over existing standard methods on 2D and 3D datasets.