Residual Deconvolutional Networks for Brain Electron Microscopy Image Segmentation

Accurate reconstruction of anatomical connections between neurons in the brain using electron microscopy (EM) images is considered to be the gold standard for circuit mapping. A key step in obtaining the reconstruction is the ability to automatically segment neurons with a precision close to human-level performance. Despite the recent technical advances in EM image segmentation, most of them rely on hand-crafted features to some extent that are specific to the data, limiting their ability to generalize. Here, we propose a simple yet powerful technique for EM image segmentation that is trained end-to-end and does not rely on prior knowledge of the data. Our proposed residual deconvolutional network consists of two information pathways that capture full-resolution features and contextual information, respectively. We showed that the proposed model is very effective in achieving the conflicting goals in dense output prediction; namely preserving full-resolution predictions and including sufficient contextual information. We applied our method to the ongoing open challenge of 3D neurite segmentation in EM images. Our method achieved one of the top results on this open challenge. We demonstrated the generality of our technique by evaluating it on the 2D neurite segmentation challenge dataset where consistently high performance was obtained. We thus expect our method to generalize well to other dense output prediction problems.