DeepPartitioning: Deep Learning of Graph Partitioning for Neuron Segmentation from Electron Microscopy Volume via Graph Neural Network

Superpixel aggregation represents a highly effective approach for automated neuron segmentation from electron microscopy (EM) volumes, which can be considered as a graph partitioning task on the region adjacency graph (RAG) of extracted superpixels. However, existing graph partitioning models for superpixel aggregation suffer from the modeling error due to insufficient model capacity. More specifically, the modeling error is caused by the simplification in formulating the real-world graph partitioning task (i.e., superpixel aggregation) into a mathematically well-defined optimization problem. To address this issue, we sidestep the explicit formulation and propose a fully end-to-end superpixel aggregation method based on deep learning of the graph partitioning task, called Deep-Partitioning. The central challenge lies in characterizing the partitioning task involving combinatorial complexity. Hence, our method incorporates a line graph neural network (LGNN) to capture higher-order relational structures in RAGs. Specifically, the LGNN enables the propagation of second-order superpixel-pair features among adjacent edges in RAGs. In this way, the partitioning task can be implicitly transformed into the vanilla second-order multicut problem while maintaining higher-order structural information. Overall, our method integrates a second-order feature extractor, a higher-order feature integrator (i.e., the LGNN), and a differentiable approximation to a multicut solver into a unified, learnable framework. Extensive experiments on three public EM datasets demonstrate the effectiveness of the proposed DeepPartitioning within the neuron segmentation pipeline.