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Ultrasound is widely used in clinical practice due to its affordability, portability, and safety. However, current AI research often overlooks combined disease prediction and tissue segmentation. We propose UniUSNet, a universal framework for ultrasound image classification and segmentation. This model handles various ultrasound types, anatomical positions, and input formats, excelling in both segmentation and classification tasks. Trained on a comprehensive dataset with over 9.7K annotations from 7 distinct anatomical positions, our model matches state-of-the-art performance and surpasses single-dataset and ablated models. Zero-shot and fine-tuning experiments show strong generalization and adaptability with minimal fine-tuning. We plan to expand our dataset and refine the prompting mechanism, with model weights and code available at (https://github.com/Zehui-Lin/UniUSNet)., Comment: Accepted to BIBM 2024

This research presents a novel method using an adversarial neural network to solve the eigenvalue topology optimization problems. The study focuses on optimizing the first eigenvalues of second-order elliptic and fourth-order biharmonic operators subject to geometry constraints. These models are usually solved with topology optimization algorithms based on sensitivity analysis, in which it is expensive to repeatedly solve the nonlinear constrained eigenvalue problem with traditional numerical methods such as finite elements or finite differences. In contrast, our method leverages automatic differentiation within the deep learning framework. Furthermore, the adversarial neural networks enable different neural networks to train independently, which improves the training efficiency and achieve satisfactory optimization results. Numerical results are presented to verify effectiveness of the algorithms for maximizing and minimizing the first eigenvalues.

Fetal pose estimation in 3D ultrasound (US) involves identifying a set of associated fetal anatomical landmarks. Its primary objective is to provide comprehensive information about the fetus through landmark connections, thus benefiting various critical applications, such as biometric measurements, plane localization, and fetal movement monitoring. However, accurately estimating the 3D fetal pose in US volume has several challenges, including poor image quality, limited GPU memory for tackling high dimensional data, symmetrical or ambiguous anatomical structures, and considerable variations in fetal poses. In this study, we propose a novel 3D fetal pose estimation framework (called FetusMapV2) to overcome the above challenges. Our contribution is three-fold. First, we propose a heuristic scheme that explores the complementary network structure-unconstrained and activation-unreserved GPU memory management approaches, which can enlarge the input image resolution for better results under limited GPU memory. Second, we design a novel Pair Loss to mitigate confusion caused by symmetrical and similar anatomical structures. It separates the hidden classification task from the landmark localization task and thus progressively eases model learning. Last, we propose a shape priors-based self-supervised learning by selecting the relatively stable landmarks to refine the pose online. Extensive experiments and diverse applications on a large-scale fetal US dataset including 1000 volumes with 22 landmarks per volume demonstrate that our method outperforms other strong competitors., Comment: 16 pages, 11 figures, accepted by Medical Image Analysis(2023)

Ultrasound (US) image segmentation is an active research area that requires real-time and highly accurate analysis in many scenarios. The detect-to-segment (DTS) frameworks have been recently proposed to balance accuracy and efficiency. However, existing approaches may suffer from inadequate contour encoding or fail to effectively leverage the encoded results. In this paper, we introduce a novel Fourier-anchor-based DTS framework called Fourier Feature Pyramid Network (FFPN) to address the aforementioned issues. The contributions of this paper are two fold. First, the FFPN utilizes Fourier Descriptors to adequately encode contours. Specifically, it maps Fourier series with similar amplitudes and frequencies into the same layer of the feature map, thereby effectively utilizing the encoded Fourier information. Second, we propose a Contour Sampling Refinement (CSR) module based on the contour proposals and refined features produced by the FFPN. This module extracts rich features around the predicted contours to further capture detailed information and refine the contours. Extensive experimental results on three large and challenging datasets demonstrate that our method outperforms other DTS methods in terms of accuracy and efficiency. Furthermore, our framework can generalize well to other detection or segmentation tasks., Comment: 10 pages, 5 figures, Accepted by MLMI 2023

Ultrasound (US) imaging is a popular tool in clinical diagnosis, offering safety, repeatability, and real-time capabilities. Freehand 3D US is a technique that provides a deeper understanding of scanned regions without increasing complexity. However, estimating elevation displacement and accumulation error remains challenging, making it difficult to infer the relative position using images alone. The addition of external lightweight sensors has been proposed to enhance reconstruction performance without adding complexity, which has been shown to be beneficial. We propose a novel online self-consistency network (OSCNet) using multiple inertial measurement units (IMUs) to improve reconstruction performance. OSCNet utilizes a modal-level self-supervised strategy to fuse multiple IMU information and reduce differences between reconstruction results obtained from each IMU data. Additionally, a sequence-level self-consistency strategy is proposed to improve the hierarchical consistency of prediction results among the scanning sequence and its sub-sequences. Experiments on large-scale arm and carotid datasets with multiple scanning tactics demonstrate that our OSCNet outperforms previous methods, achieving state-of-the-art reconstruction performance., Comment: Accepted by MICCAI-2023

Deep classifiers may encounter significant performance degradation when processing unseen testing data from varying centers, vendors, and protocols. Ensuring the robustness of deep models against these domain shifts is crucial for their widespread clinical application. In this study, we propose a novel approach called Fourier Test-time Adaptation (FTTA), which employs a dual-adaptation design to integrate input and model tuning, thereby jointly improving the model robustness. The main idea of FTTA is to build a reliable multi-level consistency measurement of paired inputs for achieving self-correction of prediction. Our contribution is two-fold. First, we encourage consistency in global features and local attention maps between the two transformed images of the same input. Here, the transformation refers to Fourier-based input adaptation, which can transfer one unseen image into source style to reduce the domain gap. Furthermore, we leverage style-interpolated images to enhance the global and local features with learnable parameters, which can smooth the consistency measurement and accelerate convergence. Second, we introduce a regularization technique that utilizes style interpolation consistency in the frequency space to encourage self-consistency in the logit space of the model output. This regularization provides strong self-supervised signals for robustness enhancement. FTTA was extensively validated on three large classification datasets with different modalities and organs. Experimental results show that FTTA is general and outperforms other strong state-of-the-art methods., Comment: Accepted by MICCAI 2023

The Segment Anything Model (SAM) is the first foundation model for general image segmentation. It has achieved impressive results on various natural image segmentation tasks. However, medical image segmentation (MIS) is more challenging because of the complex modalities, fine anatomical structures, uncertain and complex object boundaries, and wide-range object scales. To fully validate SAM's performance on medical data, we collected and sorted 53 open-source datasets and built a large medical segmentation dataset with 18 modalities, 84 objects, 125 object-modality paired targets, 1050K 2D images, and 6033K masks. We comprehensively analyzed different models and strategies on the so-called COSMOS 1050K dataset. Our findings mainly include the following: 1) SAM showed remarkable performance in some specific objects but was unstable, imperfect, or even totally failed in other situations. 2) SAM with the large ViT-H showed better overall performance than that with the small ViT-B. 3) SAM performed better with manual hints, especially box, than the Everything mode. 4) SAM could help human annotation with high labeling quality and less time. 5) SAM was sensitive to the randomness in the center point and tight box prompts, and may suffer from a serious performance drop. 6) SAM performed better than interactive methods with one or a few points, but will be outpaced as the number of points increases. 7) SAM's performance correlated to different factors, including boundary complexity, intensity differences, etc. 8) Finetuning the SAM on specific medical tasks could improve its average DICE performance by 4.39% and 6.68% for ViT-B and ViT-H, respectively. We hope that this comprehensive report can help researchers explore the potential of SAM applications in MIS, and guide how to appropriately use and develop SAM., Comment: Accepted by Medical Image Analysis. 23 pages, 18 figures, 8 tables

Deep segmentation models often face the failure risks when the testing image presents unseen distributions. Improving model robustness against these risks is crucial for the large-scale clinical application of deep models. In this study, inspired by human learning cycle, we propose a novel online reflective learning framework (RefSeg) to improve segmentation robustness. Based on the reflection-on-action conception, our RefSeg firstly drives the deep model to take action to obtain semantic segmentation. Then, RefSeg triggers the model to reflect itself. Because making deep models realize their segmentation failures during testing is challenging, RefSeg synthesizes a realistic proxy image from the semantic mask to help deep models build intuitive and effective reflections. This proxy translates and emphasizes the segmentation flaws. By maximizing the structural similarity between the raw input and the proxy, the reflection-on-action loop is closed with segmentation robustness improved. RefSeg runs in the testing phase and is general for segmentation models. Extensive validation on three medical image segmentation tasks with a public cardiac MR dataset and two in-house large ultrasound datasets show that our RefSeg remarkably improves model robustness and reports state-of-the-art performance over strong competitors., Comment: Accepted by MICCAI 2022

Ultrasound (US) is widely used for its advantages of real-time imaging, radiation-free and portability. In clinical practice, analysis and diagnosis often rely on US sequences rather than a single image to obtain dynamic anatomical information. This is challenging for novices to learn because practicing with adequate videos from patients is clinically unpractical. In this paper, we propose a novel framework to synthesize high-fidelity US videos. Specifically, the synthesis videos are generated by animating source content images based on the motion of given driving videos. Our highlights are three-fold. First, leveraging the advantages of self- and fully-supervised learning, our proposed system is trained in weakly-supervised manner for keypoint detection. These keypoints then provide vital information for handling complex high dynamic motions in US videos. Second, we decouple content and texture learning using the dual decoders to effectively reduce the model learning difficulty. Last, we adopt the adversarial training strategy with GAN losses for further improving the sharpness of the generated videos, narrowing the gap between real and synthesis videos. We validate our method on a large in-house pelvic dataset with high dynamic motion. Extensive evaluation metrics and user study prove the effectiveness of our proposed method., Comment: Accepted by MICCAI 2022

Regression learning is classic and fundamental for medical image analysis. It provides the continuous mapping for many critical applications, like the attribute estimation, object detection, segmentation and non-rigid registration. However, previous studies mainly took the case-wise criteria, like the mean square errors, as the optimization objectives. They ignored the very important population-wise correlation criterion, which is exactly the final evaluation metric in many tasks. In this work, we propose to revisit the classic regression tasks with novel investigations on directly optimizing the fine-grained correlation losses. We mainly explore two complementary correlation indexes as learnable losses: Pearson linear correlation (PLC) and Spearman rank correlation (SRC). The contributions of this paper are two folds. First, for the PLC on global level, we propose a strategy to make it robust against the outliers and regularize the key distribution factors. These efforts significantly stabilize the learning and magnify the efficacy of PLC. Second, for the SRC on local level, we propose a coarse-to-fine scheme to ease the learning of the exact ranking order among samples. Specifically, we convert the learning for the ranking of samples into the learning of similarity relationships among samples. We extensively validate our method on two typical ultrasound image regression tasks, including the image quality assessment and bio-metric measurement. Experiments prove that, with the fine-grained guidance in directly optimizing the correlation, the regression performances are significantly improved. Our proposed correlation losses are general and can be extended to more important applications., Comment: Accepted by MICCAI 2022

Ultrasound (US) imaging is widely used for anatomical structure inspection in clinical diagnosis. The training of new sonographers and deep learning based algorithms for US image analysis usually requires a large amount of data. However, obtaining and labeling large-scale US imaging data are not easy tasks, especially for diseases with low incidence. Realistic US image synthesis can alleviate this problem to a great extent. In this paper, we propose a generative adversarial network (GAN) based image synthesis framework. Our main contributions include: 1) we present the first work that can synthesize realistic B-mode US images with high-resolution and customized texture editing features; 2) to enhance structural details of generated images, we propose to introduce auxiliary sketch guidance into a conditional GAN. We superpose the edge sketch onto the object mask and use the composite mask as the network input; 3) to generate high-resolution US images, we adopt a progressive training strategy to gradually generate high-resolution images from low-resolution images. In addition, a feature loss is proposed to minimize the difference of high-level features between the generated and real images, which further improves the quality of generated images; 4) the proposed US image synthesis method is quite universal and can also be generalized to the US images of other anatomical structures besides the three ones tested in our study (lung, hip joint, and ovary); 5) extensive experiments on three large US image datasets are conducted to validate our method. Ablation studies, customized texture editing, user studies, and segmentation tests demonstrate promising results of our method in synthesizing realistic US images., Comment: Accepted by Medical Image Analysis (13 figures, 4 tabels)

3D ultrasound (US) is widely used for its rich diagnostic information. However, it is criticized for its limited field of view. 3D freehand US reconstruction is promising in addressing the problem by providing broad range and freeform scan. The existing deep learning based methods only focus on the basic cases of skill sequences, and the model relies on the training data heavily. The sequences in real clinical practice are a mix of diverse skills and have complex scanning paths. Besides, deep models should adapt themselves to the testing cases with prior knowledge for better robustness, rather than only fit to the training cases. In this paper, we propose a novel approach to sensorless freehand 3D US reconstruction considering the complex skill sequences. Our contribution is three-fold. First, we advance a novel online learning framework by designing a differentiable reconstruction algorithm. It realizes an end-to-end optimization from section sequences to the reconstructed volume. Second, a self-supervised learning method is developed to explore the context information that reconstructed by the testing data itself, promoting the perception of the model. Third, inspired by the effectiveness of shape prior, we also introduce adversarial training to strengthen the learning of anatomical shape prior in the reconstructed volume. By mining the context and structural cues of the testing data, our online learning methods can drive the model to handle complex skill sequences. Experimental results on developmental dysplasia of the hip US and fetal US datasets show that, our proposed method can outperform the start-of-the-art methods regarding the shift errors and path similarities., Comment: Early accepted by MICCAI-2021

The ultrasound (US) screening of the infant hip is vital for the early diagnosis of developmental dysplasia of the hip (DDH). The US diagnosis of DDH refers to measuring alpha and beta angles that quantify hip joint development. These two angles are calculated from key anatomical landmarks and structures of the hip. However, this measurement process is not trivial for sonographers and usually requires a thorough understanding of complex anatomical structures. In this study, we propose a multi-task framework to learn the relationships among landmarks and structures jointly and automatically evaluate DDH. Our multi-task networks are equipped with three novel modules. Firstly, we adopt Mask R-CNN as the basic framework to detect and segment key anatomical structures and add one landmark detection branch to form a new multi-task framework. Secondly, we propose a novel shape similarity loss to refine the incomplete anatomical structure prediction robustly and accurately. Thirdly, we further incorporate the landmark-structure consistent prior to ensure the consistency of the bony rim estimated from the segmented structure and the detected landmark. In our experiments, 1,231 US images of the infant hip from 632 patients are collected, of which 247 images from 126 patients are tested. The average errors in alpha and beta angles are 2.221 degrees and 2.899 degrees. About 93% and 85% estimates of alpha and beta angles have errors less than 5 degrees, respectively. Experimental results demonstrate that the proposed method can accurately and robustly realize the automatic evaluation of DDH, showing great potential for clinical application., Comment: Accepted by IEEE Journal of Biomedical and Health Informatics. 14 pages, 10 figures and 10 tables