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1. Structure-Aware Image Segmentation with Homotopy Warping

   Hu, Xiaoling (December 2022, The Thirty-sixth Conference on Neural Information Processing Systems)

   Besides per-pixel accuracy, topological correctness is also crucial for the segmentation of images with fine-scale structures, e.g., satellite images and biomedical images. In this paper, by leveraging the theory of digital topology, we identify pixels in an image that are critical for topology. By focusing on these critical pixels, we propose a new homotopy warping loss to train deep image segmentation networks for better topological accuracy. To efficiently identify these topologically critical pixels, we propose a new algorithm exploiting the distance transform. The proposed algorithm, as well as the loss function, naturally generalize to different topological structures in both 2D and 3D settings. The proposed loss function helps deep nets achieve better performance in terms of topology-aware metrics, outperforming state-of-the-art structure/topology-aware segmentation methods. 

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2. Point-Unet: A Context-Aware Point-Based Neural Network for Volumetric Segmentation

   https://doi.org/10.1007/978-3-030-87193-2_61  

   Le, Thi Hoang (September 2021, Lecture notes in computer science)

   Medical image analysis using deep learning has recently been prevalent, showing great performance for various downstream tasks including medical image segmentation and its sibling, volumetric image segmentation. Particularly, a typical volumetric segmentation network strongly relies on a voxel grid representation which treats volumetric data as a stack of individual voxel `slices', which allows learning to segment a voxel grid to be as straightforward as extending existing image-based segmentation networks to the 3D domain. However, using a voxel grid representation requires a large memory footprint, expensive test-time and limiting the scalability of the solutions. In this paper, we propose Point-Unet, a novel method that incorporates the eciency of deep learning with 3D point clouds into volumetric segmentation. Our key idea is to rst predict the regions of interest in the volume by learning an attentional probability map, which is then used for sampling the volume into a sparse point cloud that is subsequently segmented using a point-based neural network. We have conducted the experiments on the medical volumetric segmentation task with both a small-scale dataset Pancreas and large-scale datasets BraTS18, BraTS19, and BraTS20 challenges. A comprehensive benchmark on dierent metrics has shown that our context-aware Point-Unet robustly outperforms the SOTA voxel-based networks at both accuracies, memory usage during training, and time consumption during testing. 

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3. Votenet++: Registration Refinement For Multi-Atlas Segmentation

   https://doi.org/10.1109/ISBI48211.2021.9434031  

   Ding, Zhipeng; Niethammer, Marc (April 2021, International Symposium on Biomedical Imaging)

   Multi-atlas segmentation (MAS) is a popular image segmentation technique for medical images. In this work, we improve the performance of MAS by correcting registration errors before label fusion. Specifically, we use a volumetric displacement field to refine registrations based on image anatomical appearance and predicted labels. We show the influence of the initial spatial alignment as well as the beneficial effect of using label information for MAS performance. Experiments demonstrate that the proposed refinement approach improves MAS performance on a 3D magnetic resonance dataset of the knee. 

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4. Narrow Band Active Contour Attention Model for Medical Segmentation

   https://doi.org/10.3390/diagnostics11081393  

   Le, Ngan; Bui, Toan; Vo-Ho, Viet-Khoa; Yamazaki, Kashu; Luu, Khoa (August 2021, Diagnostics)

   Medical image segmentation is one of the most challenging tasks in medical image analysis and widely developed for many clinical applications. While deep learning-based approaches have achieved impressive performance in semantic segmentation, they are limited to pixel-wise settings with imbalanced-class data problems and weak boundary object segmentation in medical images. In this paper, we tackle those limitations by developing a new two-branch deep network architecture which takes both higher level features and lower level features into account. The first branch extracts higher level feature as region information by a common encoder-decoder network structure such as Unet and FCN, whereas the second branch focuses on lower level features as support information around the boundary and processes in parallel to the first branch. Our key contribution is the second branch named Narrow Band Active Contour (NB-AC) attention model which treats the object contour as a hyperplane and all data inside a narrow band as support information that influences the position and orientation of the hyperplane. Our proposed NB-AC attention model incorporates the contour length with the region energy involving a fixed-width band around the curve or surface. The proposed network loss contains two fitting terms: (i) a high level feature (i.e., region) fitting term from the first branch; (ii) a lower level feature (i.e., contour) fitting term from the second branch including the (ii1) length of the object contour and (ii2) regional energy functional formed by the homogeneity criterion of both the inner band and outer band neighboring the evolving curve or surface. The proposed NB-AC loss can be incorporated into both 2D and 3D deep network architectures. The proposed network has been evaluated on different challenging medical image datasets, including DRIVE, iSeg17, MRBrainS18 and Brats18. The experimental results have shown that the proposed NB-AC loss outperforms other mainstream loss functions: Cross Entropy, Dice, Focal on two common segmentation frameworks Unet and FCN. Our 3D network which is built upon the proposed NB-AC loss and 3DUnet framework achieved state-of-the-art results on multiple volumetric datasets. 

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5. A Topological-Attention ConvLSTM Network and Its Application to EM Images

   https://doi.org/10.1007/978-3-030-87193-2_21  

   Yang, Jiaqi; Hu, Xiaoling; Chen, Chao; Tsai, Chialing (October 2021, Medical Image Computing and Computer Assisted Intervention (MICCAI))

   Structural accuracy of segmentation is important for fine-scale structures in biomedical images. We propose a novel Topological-Attention ConvLSTM Network (TACLNet) for 3D anisotropic image segmentation with high structural accuracy. We adopt ConvLSTM to leverage contextual information from adjacent slices while achieving high efficiency. We propose a Spatial Topological-Attention (STA) module to effectively transfer topologically critical information across slices. Furthermore, we propose an Iterative Topological-Attention (ITA) module that provides a more stable topologically critical map for segmentation. Quantitative and qualitative results show that our proposed method outperforms various baselines in terms of topology-aware evaluation metrics. 

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