Improving 3D Medical Image Segmentation at Boundary Regions using Local Self-attention and Global Volume Mixing

Volumetric medical image segmentation is a fundamental problem in medical image analysis where the objective is to accurately classify a given 3D volumetric medical image with voxel-level precision. In this work, we propose a novel hierarchical encoder-decoder-based framework that strives to explicitly capture the local and global dependencies for volumetric 3D medical image segmentation. The proposed framework exploits local volume-based self-attention to encode the local dependencies at high resolution and introduces a novel volumetric MLP-mixer to capture the global dependencies at low-resolution feature representations, respectively. The proposed volumetric MLP-mixer learns better associations among volumetric feature representations. These explicit local and global feature representations contribute to better learning of the shape-boundary characteristics of the organs. Extensive experiments on three different datasets reveal that the proposed method achieves favorable performance compared to state-of-the-art approaches. On the challenging Synapse Multi-organ dataset, the proposed method achieves an absolute 3.82\% gain over the state-of-the-art approaches in terms of HD95 evaluation metrics {while a similar improvement pattern is exhibited in MSD Liver and Pancreas tumor datasets}. We also provide a detailed comparison between recent architectural design choices in the 2D computer vision literature by adapting them for the problem of 3D medical image segmentation. Finally, our experiments on the ZebraFish 3D cell membrane dataset having limited training data demonstrate the superior transfer learning capabilities of the proposed vMixer model on the challenging 3D cell instance segmentation task, where accurate boundary prediction plays a vital role in distinguishing individual cell instances.

Medical Image Segmentation Using Directional Window Attention

Accurate segmentation of medical images is crucial for diagnostic purposes, including cell segmentation, tumor identification, and organ localization. Traditional convolutional neural network (CNN)-based approaches struggled to achieve precise segmentation results due to their limited receptive fields, particularly in cases involving multi-organ segmentation with varying shapes and sizes. The transformer-based approaches address this limitation by leveraging the global receptive field, but they often face challenges in capturing local information required for pixel-precise segmentation. In this work, we introduce DwinFormer, a hierarchical encoder-decoder architecture for medical image segmentation comprising a directional window (Dwin) attention and global self-attention (GSA) for feature encoding. The focus of our design is the introduction of Dwin block within DwinFormer that effectively captures local and global information along the horizontal, vertical, and depthwise directions of the input feature map by separately performing attention in each of these directional volumes. To this end, our Dwin block introduces a nested Dwin attention (NDA) that progressively increases the receptive field in horizontal, vertical, and depthwise directions and a convolutional Dwin attention (CDA) that captures local contextual information for the attention computation. While the proposed Dwin block captures local and global dependencies at the first two high-resolution stages of DwinFormer, the GSA block encodes global dependencies at the last two lower-resolution stages. Experiments over the challenging 3D Synapse Multi-organ dataset and Cell HMS dataset demonstrate the benefits of our DwinFormer over the state-of-the-art approaches. Our source code will be publicly available at \url{https://github.com/Daniyanaj/DWINFORMER}.