AM-UNet: automated mini 3D end-to-end U-net based network for brain claustrum segmentation

Abstract

Recent advances in deep learning (DL) have provided promising solutions to medical image segmentation. Among existing segmentation approaches, the U-Net-based methods have been used widely. However, very few U-Net-based studies have been conducted on automatic segmentation of the human brain claustrum (CL). The CL segmentation is challenging due to its thin, sheet-like structure, heterogeneity of its image modalities and formats, imperfect labels, and data imbalance. We propose an automatic optimized U-Net-based 3D segmentation model, called AM-UNet, designed as an end-to-end process of the pre and post-process techniques and a U-Net model for CL segmentation. It is a lightweight and scalable solution which has achieved the state-of-the-art accuracy for automatic CL segmentation on 3D magnetic resonance images (MRI). On the T1/T2 combined MRI CL dataset, AM-UNet has obtained excellent results, including Dice, Intersection over Union (IoU), and Intraclass Correlation Coefficient (ICC) scores of 82%, 70%, and 90%, respectively. We have conducted the comparative evaluation of AM-UNet with other pre-existing models for segmentation on the MRI CL dataset. As a result, medical experts confirmed the superiority of the proposed AM-UNet model for automatic CL segmentation. The source code and model of the AM-UNet project is publicly available on GitHub: https://github.com/AhmedAlbishri/AM-UNET.