CAN3D: Fast 3D medical image segmentation via compact context aggregation

计算机科学 内存占用 分割 卷积神经网络 工作站 背景(考古学) 人工智能 深度学习 推论 图像分割 医学影像学 计算机视觉 计算机工程 生物 操作系统 古生物学
作者
Wei Dai,Boyeong Woo,Siyu Liu,Matthew Marques,Craig Engstrom,Peter Greer,Stuart Crozier,Jason Dowling,Shekhar S. Chandra
出处
期刊:Medical Image Analysis [Elsevier BV]
卷期号:82: 102562-102562 被引量:4
标识
DOI:10.1016/j.media.2022.102562
摘要

Direct automatic segmentation of objects in 3D medical imaging, such as magnetic resonance (MR) imaging, is challenging as it often involves accurately identifying multiple individual structures with complex geometries within a large volume under investigation. Most deep learning approaches address these challenges by enhancing their learning capability through a substantial increase in trainable parameters within their models. An increased model complexity will incur high computational costs and large memory requirements unsuitable for real-time implementation on standard clinical workstations, as clinical imaging systems typically have low-end computer hardware with limited memory and CPU resources only. This paper presents a compact convolutional neural network (CAN3D) designed specifically for clinical workstations and allows the segmentation of large 3D Magnetic Resonance (MR) images in real-time. The proposed CAN3D has a shallow memory footprint to reduce the number of model parameters and computer memory required for state-of-the-art performance and maintain data integrity by directly processing large full-size 3D image input volumes with no patches required. The proposed architecture significantly reduces computational costs, especially for inference using the CPU. We also develop a novel loss function with extra shape constraints to improve segmentation accuracy for imbalanced classes in 3D MR images. Compared to state-of-the-art approaches (U-Net3D, improved U-Net3D and V-Net), CAN3D reduced the number of parameters up to two orders of magnitude and achieved much faster inference, up to 5 times when predicting with a standard commercial CPU (instead of GPU). For the open-access OAI-ZIB knee MR dataset, in comparison with manual segmentation, CAN3D achieved Dice coefficient values of (mean = 0.87 ± 0.02 and 0.85 ± 0.04) with mean surface distance errors (mean = 0.36 ± 0.32 mm and 0.29 ± 0.10 mm) for imbalanced classes such as (femoral and tibial) cartilage volumes respectively when training volume-wise under only 12G video memory. Similarly, CAN3D demonstrated high accuracy and efficiency on a pelvis 3D MR imaging dataset for prostate cancer consisting of 211 examinations with expert manual semantic labels (bladder, body, bone, rectum, prostate) now released publicly for scientific use as part of this work.
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