arXiv subjects

Dong Ni

Publications and source records attributed to Dong Ni.

At least 55 records · Page 3Linked to original sources

arXiv2024

Efficient MedSAMs: Segment Anything in Medical Images on Laptop

Promptable segmentation foundation models have emerged as a transformative approach to addressing the diverse needs in medical images, but most existing models require expensive computing, posing a big barrier to their adoption in clinical practice. In this work, we organized the first international competition dedicated to promptable medical image segmentation, featuring a large-scale dataset spanning nine common imaging modalities from over 20 different institutions. The top teams developed lightweight segmentation foundation models and implemented an efficient inference pipeline that substantially reduced computational requirements while maintaining state-of-the-art segmentation accuracy. Moreover, the post-challenge phase advanced the algorithms through the design of performance booster and reproducibility tasks, resulting in improved algorithms and validated reproducibility of the winning solution. Furthermore, the best-performing algorithms have been incorporated into the open-source software with a user-friendly interface to facilitate clinical adoption. The data and code are publicly available to foster the further development of medical image segmentation foundation models and pave the way for impactful real-world applications.

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arXiv2024

Mitral Regurgitation Recognition based on Unsupervised Out-of-Distribution Detection with Residual Diffusion Amplification

Mitral regurgitation (MR) is a serious heart valve disease. Early and accurate diagnosis of MR via ultrasound video is critical for timely clinical decision-making and surgical intervention. However, manual MR diagnosis heavily relies on the operator's experience, which may cause misdiagnosis and inter-observer variability. Since MR data is limited and has large intra-class variability, we propose an unsupervised out-of-distribution (OOD) detection method to identify MR rather than building a deep classifier. To our knowledge, we are the first to explore OOD in MR ultrasound videos. Our method consists of a feature extractor, a feature reconstruction model, and a residual accumulation amplification algorithm. The feature extractor obtains features from the video clips and feeds them into the feature reconstruction model to restore the original features. The residual accumulation amplification algorithm then iteratively performs noise feature reconstruction, amplifying the reconstructed error of OOD features. This algorithm is straightforward yet efficient and can seamlessly integrate as a plug-and-play component in reconstruction-based OOD detection methods. We validated the proposed method on a large ultrasound dataset containing 893 non-MR and 267 MR videos. Experimental results show that our OOD detection method can effectively identify MR samples.

cs.CV↗

arXiv2024

FiRework: Field Refinement Framework for Efficient Enhancement of Deformable Registration

Deformable image registration remains a fundamental task in clinical practice, yet solving registration problems involving complex deformations remains challenging. Current deep learning-based registration methods employ continuous deformation to model large deformations, which often suffer from accumulated registration errors and interpolation inaccuracies. Moreover, achieving satisfactory results with these frameworks typically requires a large number of cascade stages, demanding substantial computational resources. Therefore, we propose a novel approach, the field refinement framework (FiRework), tailored for unsupervised deformable registration, aiming to address these challenges. In FiRework, we redesign the continuous deformation framework to mitigate the aforementioned errors. Notably, our FiRework requires only one level of recursion during training and supports continuous inference, offering improved efficacy compared to continuous deformation frameworks. We conducted experiments on two brain MRI datasets, enhancing two existing deformable registration networks with FiRework. The experimental results demonstrate the superior performance of our proposed framework in deformable registration. The code is publicly available at https://github.com/ZAX130/FiRework.

cs.CV↗

arXiv2024

A Narrative Review of Image Processing Techniques Related to Prostate Ultrasound

Prostate cancer (PCa) poses a significant threat to men's health, with early diagnosis being crucial for improving prognosis and reducing mortality rates. Transrectal ultrasound (TRUS) plays a vital role in the diagnosis and image-guided intervention of PCa.To facilitate physicians with more accurate and efficient computer-assisted diagnosis and interventions, many image processing algorithms in TRUS have been proposed and achieved state-of-the-art performance in several tasks, including prostate gland segmentation, prostate image registration, PCa classification and detection, and interventional needle detection. The rapid development of these algorithms over the past two decades necessitates a comprehensive summary. In consequence, this survey provides a \textcolor{blue}{narrative } analysis of this field, outlining the evolution of image processing methods in the context of TRUS image analysis and meanwhile highlighting their relevant contributions. Furthermore, this survey discusses current challenges and suggests future research directions to possibly advance this field further.

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arXiv2024

EM-Net: Efficient Channel and Frequency Learning with Mamba for 3D Medical Image Segmentation

Convolutional neural networks have primarily led 3D medical image segmentation but may be limited by small receptive fields. Transformer models excel in capturing global relationships through self-attention but are challenged by high computational costs at high resolutions. Recently, Mamba, a state space model, has emerged as an effective approach for sequential modeling. Inspired by its success, we introduce a novel Mamba-based 3D medical image segmentation model called EM-Net. It not only efficiently captures attentive interaction between regions by integrating and selecting channels, but also effectively utilizes frequency domain to harmonize the learning of features across varying scales, while accelerating training speed. Comprehensive experiments on two challenging multi-organ datasets with other state-of-the-art (SOTA) algorithms show that our method exhibits better segmentation accuracy while requiring nearly half the parameter size of SOTA models and 2x faster training speed.

cs.CV↗

arXiv2024

PSFHS Challenge Report: Pubic Symphysis and Fetal Head Segmentation from Intrapartum Ultrasound Images

Segmentation of the fetal and maternal structures, particularly intrapartum ultrasound imaging as advocated by the International Society of Ultrasound in Obstetrics and Gynecology (ISUOG) for monitoring labor progression, is a crucial first step for quantitative diagnosis and clinical decision-making. This requires specialized analysis by obstetrics professionals, in a task that i) is highly time- and cost-consuming and ii) often yields inconsistent results. The utility of automatic segmentation algorithms for biometry has been proven, though existing results remain suboptimal. To push forward advancements in this area, the Grand Challenge on Pubic Symphysis-Fetal Head Segmentation (PSFHS) was held alongside the 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023). This challenge aimed to enhance the development of automatic segmentation algorithms at an international scale, providing the largest dataset to date with 5,101 intrapartum ultrasound images collected from two ultrasound machines across three hospitals from two institutions. The scientific community's enthusiastic participation led to the selection of the top 8 out of 179 entries from 193 registrants in the initial phase to proceed to the competition's second stage. These algorithms have elevated the state-of-the-art in automatic PSFHS from intrapartum ultrasound images. A thorough analysis of the results pinpointed ongoing challenges in the field and outlined recommendations for future work. The top solutions and the complete dataset remain publicly available, fostering further advancements in automatic segmentation and biometry for intrapartum ultrasound imaging.

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arXiv2024

UniUSNet: A Promptable Framework for Universal Ultrasound Disease Prediction and Tissue Segmentation

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).

cs.CV↗

arXiv2024

Semi-Supervised Dual-Stream Self-Attentive Adversarial Graph Contrastive Learning for Cross-Subject EEG-based Emotion Recognition

Electroencephalography (EEG) is an objective tool for emotion recognition with promising applications. However, the scarcity of labeled data remains a major challenge in this field, limiting the widespread use of EEG-based emotion recognition. In this paper, a semi-supervised Dual-stream Self-Attentive Adversarial Graph Contrastive learning framework (termed as DS-AGC) is proposed to tackle the challenge of limited labeled data in cross-subject EEG-based emotion recognition. The DS-AGC framework includes two parallel streams for extracting non-structural and structural EEG features. The non-structural stream incorporates a semi-supervised multi-domain adaptation method to alleviate distribution discrepancy among labeled source domain, unlabeled source domain, and unknown target domain. The structural stream develops a graph contrastive learning method to extract effective graph-based feature representation from multiple EEG channels in a semi-supervised manner. Further, a self-attentive fusion module is developed for feature fusion, sample selection, and emotion recognition, which highlights EEG features more relevant to emotions and data samples in the labeled source domain that are closer to the target domain. Extensive experiments conducted on two benchmark databases (SEED and SEED-IV) using a semi-supervised cross-subject leave-one-subject-out cross-validation evaluation scheme show that the proposed model outperforms existing methods under different incomplete label conditions (with an average improvement of 5.83% on SEED and 6.99% on SEED-IV), demonstrating its effectiveness in addressing the label scarcity problem in cross-subject EEG-based emotion recognition.

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arXiv2024

Robust Box Prompt based SAM for Medical Image Segmentation

The Segment Anything Model (SAM) can achieve satisfactory segmentation performance under high-quality box prompts. However, SAM's robustness is compromised by the decline in box quality, limiting its practicality in clinical reality. In this study, we propose a novel Robust Box prompt based SAM (\textbf{RoBox-SAM}) to ensure SAM's segmentation performance under prompts with different qualities. Our contribution is three-fold. First, we propose a prompt refinement module to implicitly perceive the potential targets, and output the offsets to directly transform the low-quality box prompt into a high-quality one. We then provide an online iterative strategy for further prompt refinement. Second, we introduce a prompt enhancement module to automatically generate point prompts to assist the box-promptable segmentation effectively. Last, we build a self-information extractor to encode the prior information from the input image. These features can optimize the image embeddings and attention calculation, thus, the robustness of SAM can be further enhanced. Extensive experiments on the large medical segmentation dataset including 99,299 images, 5 modalities, and 25 organs/targets validated the efficacy of our proposed RoBox-SAM.

cs.CV↗

arXiv2024

Explainable and Controllable Motion Curve Guided Cardiac Ultrasound Video Generation

Echocardiography video is a primary modality for diagnosing heart diseases, but the limited data poses challenges for both clinical teaching and machine learning training. Recently, video generative models have emerged as a promising strategy to alleviate this issue. However, previous methods often relied on holistic conditions during generation, hindering the flexible movement control over specific cardiac structures. In this context, we propose an explainable and controllable method for echocardiography video generation, taking an initial frame and a motion curve as guidance. Our contributions are three-fold. First, we extract motion information from each heart substructure to construct motion curves, enabling the diffusion model to synthesize customized echocardiography videos by modifying these curves. Second, we propose the structure-to-motion alignment module, which can map semantic features onto motion curves across cardiac structures. Third, The position-aware attention mechanism is designed to enhance video consistency utilizing Gaussian masks with structural position information. Extensive experiments on three echocardiography datasets show that our method outperforms others regarding fidelity and consistency. The full code will be released at https://github.com/mlmi-2024-72/ECM.

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arXiv2024

PAPM: A Physics-aware Proxy Model for Process Systems

In the context of proxy modeling for process systems, traditional data-driven deep learning approaches frequently encounter significant challenges, such as substantial training costs induced by large amounts of data, and limited generalization capabilities. As a promising alternative, physics-aware models incorporate partial physics knowledge to ameliorate these challenges. Although demonstrating efficacy, they fall short in terms of exploration depth and universality. To address these shortcomings, we introduce a physics-aware proxy model (PAPM) that fully incorporates partial prior physics of process systems, which includes multiple input conditions and the general form of conservation relations, resulting in better out-of-sample generalization. Additionally, PAPM contains a holistic temporal-spatial stepping module for flexible adaptation across various process systems. Through systematic comparisons with state-of-the-art pure data-driven and physics-aware models across five two-dimensional benchmarks in nine generalization tasks, PAPM notably achieves an average performance improvement of 6.7%, while requiring fewer FLOPs, and just 1% of the parameters compared to the prior leading method. The code is available at https://github.com/pengwei07/PAPM.

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arXiv2024

HeartBeat: Towards Controllable Echocardiography Video Synthesis with Multimodal Conditions-Guided Diffusion Models

Echocardiography (ECHO) video is widely used for cardiac examination. In clinical, this procedure heavily relies on operator experience, which needs years of training and maybe the assistance of deep learning-based systems for enhanced accuracy and efficiency. However, it is challenging since acquiring sufficient customized data (e.g., abnormal cases) for novice training and deep model development is clinically unrealistic. Hence, controllable ECHO video synthesis is highly desirable. In this paper, we propose a novel diffusion-based framework named HeartBeat towards controllable and high-fidelity ECHO video synthesis. Our highlight is three-fold. First, HeartBeat serves as a unified framework that enables perceiving multimodal conditions simultaneously to guide controllable generation. Second, we factorize the multimodal conditions into local and global ones, with two insertion strategies separately provided fine- and coarse-grained controls in a composable and flexible manner. In this way, users can synthesize ECHO videos that conform to their mental imagery by combining multimodal control signals. Third, we propose to decouple the visual concepts and temporal dynamics learning using a two-stage training scheme for simplifying the model training. One more interesting thing is that HeartBeat can easily generalize to mask-guided cardiac MRI synthesis in a few shots, showcasing its scalability to broader applications. Extensive experiments on two public datasets show the efficacy of the proposed HeartBeat.

cs.CV↗

arXiv2024

Fine-grained Context and Multi-modal Alignment for Freehand 3D Ultrasound Reconstruction

Fine-grained spatio-temporal learning is crucial for freehand 3D ultrasound reconstruction. Previous works mainly resorted to the coarse-grained spatial features and the separated temporal dependency learning and struggles for fine-grained spatio-temporal learning. Mining spatio-temporal information in fine-grained scales is extremely challenging due to learning difficulties in long-range dependencies. In this context, we propose a novel method to exploit the long-range dependency management capabilities of the state space model (SSM) to address the above challenge. Our contribution is three-fold. First, we propose ReMamba, which mines multi-scale spatio-temporal information by devising a multi-directional SSM. Second, we propose an adaptive fusion strategy that introduces multiple inertial measurement units as auxiliary temporal information to enhance spatio-temporal perception. Last, we design an online alignment strategy that encodes the temporal information as pseudo labels for multi-modal alignment to further improve reconstruction performance. Extensive experimental validations on two large-scale datasets show remarkable improvement from our method over competitors.

cs.CV↗

arXiv2024

Is Two-shot All You Need? A Label-efficient Approach for Video Segmentation in Breast Ultrasound

Breast lesion segmentation from breast ultrasound (BUS) videos could assist in early diagnosis and treatment. Existing video object segmentation (VOS) methods usually require dense annotation, which is often inaccessible for medical datasets. Furthermore, they suffer from accumulative errors and a lack of explicit space-time awareness. In this work, we propose a novel two-shot training paradigm for BUS video segmentation. It not only is able to capture free-range space-time consistency but also utilizes a source-dependent augmentation scheme. This label-efficient learning framework is validated on a challenging in-house BUS video dataset. Results showed that it gained comparable performance to the fully annotated ones given only 1.9% training labels.

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arXiv2024

Agent with Warm Start and Active Termination for Plane Localization in 3D Ultrasound

Standard plane localization is crucial for ultrasound (US) diagnosis. In prenatal US, dozens of standard planes are manually acquired with a 2D probe. It is time-consuming and operator-dependent. In comparison, 3D US containing multiple standard planes in one shot has the inherent advantages of less user-dependency and more efficiency. However, manual plane localization in US volume is challenging due to the huge search space and large fetal posture variation. In this study, we propose a novel reinforcement learning (RL) framework to automatically localize fetal brain standard planes in 3D US. Our contribution is two-fold. First, we equip the RL framework with a landmark-aware alignment module to provide warm start and strong spatial bounds for the agent actions, thus ensuring its effectiveness. Second, instead of passively and empirically terminating the agent inference, we propose a recurrent neural network based strategy for active termination of the agent's interaction procedure. This improves both the accuracy and efficiency of the localization system. Extensively validated on our in-house large dataset, our approach achieves the accuracy of 3.4mm/9.6° and 2.7mm/9.1° for the transcerebellar and transthalamic plane localization, respectively. Ourproposed RL framework is general and has the potential to improve the efficiency and standardization of US scanning.

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arXiv2024

FetusMap: Fetal Pose Estimation in 3D Ultrasound

The 3D ultrasound (US) entrance inspires a multitude of automated prenatal examinations. However, studies about the structuralized description of the whole fetus in 3D US are still rare. In this paper, we propose to estimate the 3D pose of fetus in US volumes to facilitate its quantitative analyses in global and local scales. Given the great challenges in 3D US, including the high volume dimension, poor image quality, symmetric ambiguity in anatomical structures and large variations of fetal pose, our contribution is three-fold. (i) This is the first work about 3D pose estimation of fetus in the literature. We aim to extract the skeleton of whole fetus and assign different segments/joints with correct torso/limb labels. (ii) We propose a self-supervised learning (SSL) framework to finetune the deep network to form visually plausible pose predictions. Specifically, we leverage the landmark-based registration to effectively encode case-adaptive anatomical priors and generate evolving label proxy for supervision. (iii) To enable our 3D network perceive better contextual cues with higher resolution input under limited computing resource, we further adopt the gradient check-pointing (GCP) strategy to save GPU memory and improve the prediction. Extensively validated on a large 3D US dataset, our method tackles varying fetal poses and achieves promising results. 3D pose estimation of fetus has potentials in serving as a map to provide navigation for many advanced studies.

cs.CV↗

arXiv2024

LUM-ViT: Learnable Under-sampling Mask Vision Transformer for Bandwidth Limited Optical Signal Acquisition

Bandwidth constraints during signal acquisition frequently impede real-time detection applications. Hyperspectral data is a notable example, whose vast volume compromises real-time hyperspectral detection. To tackle this hurdle, we introduce a novel approach leveraging pre-acquisition modulation to reduce the acquisition volume. This modulation process is governed by a deep learning model, utilizing prior information. Central to our approach is LUM-ViT, a Vision Transformer variant. Uniquely, LUM-ViT incorporates a learnable under-sampling mask tailored for pre-acquisition modulation. To further optimize for optical calculations, we propose a kernel-level weight binarization technique and a three-stage fine-tuning strategy. Our evaluations reveal that, by sampling a mere 10% of the original image pixels, LUM-ViT maintains the accuracy loss within 1.8% on the ImageNet classification task. The method sustains near-original accuracy when implemented on real-world optical hardware, demonstrating its practicality. Code will be available at https://github.com/MaxLLF/LUM-ViT.

cs.CV↗

arXiv2024

Deep Attentive Features for Prostate Segmentation in 3D Transrectal Ultrasound

Automatic prostate segmentation in transrectal ultrasound (TRUS) images is of essential importance for image-guided prostate interventions and treatment planning. However, developing such automatic solutions remains very challenging due to the missing/ambiguous boundary and inhomogeneous intensity distribution of the prostate in TRUS, as well as the large variability in prostate shapes. This paper develops a novel 3D deep neural network equipped with attention modules for better prostate segmentation in TRUS by fully exploiting the complementary information encoded in different layers of the convolutional neural network (CNN). Our attention module utilizes the attention mechanism to selectively leverage the multilevel features integrated from different layers to refine the features at each individual layer, suppressing the non-prostate noise at shallow layers of the CNN and increasing more prostate details into features at deep layers. Experimental results on challenging 3D TRUS volumes show that our method attains satisfactory segmentation performance. The proposed attention mechanism is a general strategy to aggregate multi-level deep features and has the potential to be used for other medical image segmentation tasks. The code is publicly available at https://github.com/wulalago/DAF3D.

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