Near Real-time Hippocampus Segmentation Using Patch-based Canonical Neural Network

Abstract: Over the past decades, state-of-the-art medical image segmentation has heavily rested on signal processing paradigms, most notably registration-based label propagation and pair-wise patch comparison, which are generally slow despite a high segmentation accuracy. In recent years, deep learning has revolutionalized computer vision with many practices outperforming prior art, in particular the convolutional neural network (CNN) studies on image classification. Deep CNN has also started being applied to medical image segmentation lately, but generally involves long training and demanding memory requirements, achieving limited success. We propose a patch-based deep learning framework based on a revisit to the classic neural network model with substantial modernization, including the use of Rectified Linear Unit (ReLU) activation, dropout layers, 2.5D tri-planar patch multi-pathway settings. In a test application to hippocampus segmentation using 100 brain MR images from the ADNI database, our approach significantly outperformed prior art in terms of both segmentation accuracy and speed: scoring a median Dice score up to 90.98% on a near real-time performance (<1s).