arXiv subjects

Dong Ni

Publications and source records attributed to Dong Ni.

At least 73 records · Page 4Linked to original sources

arXiv2024

A Foundation Model for General Moving Object Segmentation in Medical Images

Medical image segmentation aims to delineate the anatomical or pathological structures of interest, playing a crucial role in clinical diagnosis. A substantial amount of high-quality annotated data is crucial for constructing high-precision deep segmentation models. However, medical annotation is highly cumbersome and time-consuming, especially for medical videos or 3D volumes, due to the huge labeling space and poor inter-frame consistency. Recently, a fundamental task named Moving Object Segmentation (MOS) has made significant advancements in natural images. Its objective is to delineate moving objects from the background within image sequences, requiring only minimal annotations. In this paper, we propose the first foundation model, named iMOS, for MOS in medical images. Extensive experiments on a large multi-modal medical dataset validate the effectiveness of the proposed iMOS. Specifically, with the annotation of only a small number of images in the sequence, iMOS can achieve satisfactory tracking and segmentation performance of moving objects throughout the entire sequence in bi-directions. We hope that the proposed iMOS can help accelerate the annotation speed of experts, and boost the development of medical foundation models.

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arXiv2024

TriAug: Out-of-Distribution Detection for Imbalanced Breast Lesion in Ultrasound

Different diseases, such as histological subtypes of breast lesions, have severely varying incidence rates. Even trained with substantial amount of in-distribution (ID) data, models often encounter out-of-distribution (OOD) samples belonging to unseen classes in clinical reality. To address this, we propose a novel framework built upon a long-tailed OOD detection task for breast ultrasound images. It is equipped with a triplet state augmentation (TriAug) which improves ID classification accuracy while maintaining a promising OOD detection performance. Meanwhile, we designed a balanced sphere loss to handle the class imbalanced problem. Experimental results show that the model outperforms state-of-art OOD approaches both in ID classification (F1-score=42.12%) and OOD detection (AUROC=78.06%).

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arXiv2024

Thyroid ultrasound diagnosis improvement via multi-view self-supervised learning and two-stage pre-training

Thyroid nodule classification and segmentation in ultrasound images are crucial for computer-aided diagnosis; however, they face limitations owing to insufficient labeled data. In this study, we proposed a multi-view contrastive self-supervised method to improve thyroid nodule classification and segmentation performance with limited manual labels. Our method aligns the transverse and longitudinal views of the same nodule, thereby enabling the model to focus more on the nodule area. We designed an adaptive loss function that eliminates the limitations of the paired data. Additionally, we adopted a two-stage pre-training to exploit the pre-training on ImageNet and thyroid ultrasound images. Extensive experiments were conducted on a large-scale dataset collected from multiple centers. The results showed that the proposed method significantly improves nodule classification and segmentation performance with limited manual labels and outperforms state-of-the-art self-supervised methods. The two-stage pre-training also significantly exceeded ImageNet pre-training.

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arXiv2024

One-Stop Automated Diagnostic System for Carpal Tunnel Syndrome in Ultrasound Images Using Deep Learning

Objective: Ultrasound (US) examination has unique advantages in diagnosing carpal tunnel syndrome (CTS) while identifying the median nerve (MN) and diagnosing CTS depends heavily on the expertise of examiners. To alleviate this problem, we aimed to develop a one-stop automated CTS diagnosis system (OSA-CTSD) and evaluate its effectiveness as a computer-aided diagnostic tool. Methods: We combined real-time MN delineation, accurate biometric measurements, and explainable CTS diagnosis into a unified framework, called OSA-CTSD. We collected a total of 32,301 static images from US videos of 90 normal wrists and 40 CTS wrists for evaluation using a simplified scanning protocol. Results: The proposed model showed better segmentation and measurement performance than competing methods, reporting that HD95 score of 7.21px, ASSD score of 2.64px, Dice score of 85.78%, and IoU score of 76.00%, respectively. In the reader study, it demonstrated comparable performance with the average performance of the experienced in classifying the CTS, while outperformed that of the inexperienced radiologists in terms of classification metrics (e.g., accuracy score of 3.59% higher and F1 score of 5.85% higher). Conclusion: The OSA-CTSD demonstrated promising diagnostic performance with the advantages of real-time, automation, and clinical interpretability. The application of such a tool can not only reduce reliance on the expertise of examiners, but also can help to promote the future standardization of the CTS diagnosis process, benefiting both patients and radiologists.

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arXiv2024

Segment Anything Model for Medical Images?

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.

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arXiv2023

InstructVideo: Instructing Video Diffusion Models with Human Feedback

Diffusion models have emerged as the de facto paradigm for video generation. However, their reliance on web-scale data of varied quality often yields results that are visually unappealing and misaligned with the textual prompts. To tackle this problem, we propose InstructVideo to instruct text-to-video diffusion models with human feedback by reward fine-tuning. InstructVideo has two key ingredients: 1) To ameliorate the cost of reward fine-tuning induced by generating through the full DDIM sampling chain, we recast reward fine-tuning as editing. By leveraging the diffusion process to corrupt a sampled video, InstructVideo requires only partial inference of the DDIM sampling chain, reducing fine-tuning cost while improving fine-tuning efficiency. 2) To mitigate the absence of a dedicated video reward model for human preferences, we repurpose established image reward models, e.g., HPSv2. To this end, we propose Segmental Video Reward, a mechanism to provide reward signals based on segmental sparse sampling, and Temporally Attenuated Reward, a method that mitigates temporal modeling degradation during fine-tuning. Extensive experiments, both qualitative and quantitative, validate the practicality and efficacy of using image reward models in InstructVideo, significantly enhancing the visual quality of generated videos without compromising generalization capabilities. Code and models will be made publicly available.

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arXiv2023

From Denoising Training to Test-Time Adaptation: Enhancing Domain Generalization for Medical Image Segmentation

In medical image segmentation, domain generalization poses a significant challenge due to domain shifts caused by variations in data acquisition devices and other factors. These shifts are particularly pronounced in the most common scenario, which involves only single-source domain data due to privacy concerns. To address this, we draw inspiration from the self-supervised learning paradigm that effectively discourages overfitting to the source domain. We propose the Denoising Y-Net (DeY-Net), a novel approach incorporating an auxiliary denoising decoder into the basic U-Net architecture. The auxiliary decoder aims to perform denoising training, augmenting the domain-invariant representation that facilitates domain generalization. Furthermore, this paradigm provides the potential to utilize unlabeled data. Building upon denoising training, we propose Denoising Test Time Adaptation (DeTTA) that further: (i) adapts the model to the target domain in a sample-wise manner, and (ii) adapts to the noise-corrupted input. Extensive experiments conducted on widely-adopted liver segmentation benchmarks demonstrate significant domain generalization improvements over our baseline and state-of-the-art results compared to other methods. Code is available at https://github.com/WenRuxue/DeTTA.

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arXiv2023

FetusMapV2: Enhanced Fetal Pose Estimation in 3D Ultrasound

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.

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arXiv2023

Non-Iterative Scribble-Supervised Learning with Pacing Pseudo-Masks for Medical Image Segmentation

Scribble-supervised medical image segmentation tackles the limitation of sparse masks. Conventional approaches alternate between: labeling pseudo-masks and optimizing network parameters. However, such iterative two-stage paradigm is unwieldy and could be trapped in poor local optima since the networks undesirably regress to the erroneous pseudo-masks. To address these issues, we propose a non-iterative method where a stream of varying (pacing) pseudo-masks teach a network via consistency training, named PacingPseudo. Our motivation lies first in a non-iterative process. Interestingly, it can be achieved gracefully by a siamese architecture, wherein a stream of pseudo-masks naturally assimilate a stream of predicted masks during training. Second, we make the consistency training effective with two necessary designs: (i) entropy regularization to obtain high-confidence pseudo-masks for effective teaching; and (ii) distorted augmentations to create discrepancy between the pseudo-mask and predicted-mask streams for consistency regularization. Third, we devise a new memory bank mechanism that provides an extra source of ensemble features to complement scarce labeled pixels. The efficacy of the proposed PacingPseudo is validated on three public medical image datasets, including the segmentation tasks of abdominal multi-organs, cardiac structures, and myocardium. Extensive experiments demonstrate our PacingPseudo improves the baseline by large margins and consistently outcompetes several previous methods. In some cases, our PacingPseudo achieves comparable performance with its fully-supervised counterparts, showing the feasibility of our method for the challenging scribble-supervised segmentation applications. The code and scribble annotations will be publicly available.

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arXiv2023

PE-MED: Prompt Enhancement for Interactive Medical Image Segmentation

Interactive medical image segmentation refers to the accurate segmentation of the target of interest through interaction (e.g., click) between the user and the image. It has been widely studied in recent years as it is less dependent on abundant annotated data and more flexible than fully automated segmentation. However, current studies have not fully explored user-provided prompt information (e.g., points), including the knowledge mined in one interaction, and the relationship between multiple interactions. Thus, in this paper, we introduce a novel framework equipped with prompt enhancement, called PE-MED, for interactive medical image segmentation. First, we introduce a Self-Loop strategy to generate warm initial segmentation results based on the first prompt. It can prevent the highly unfavorable scenarios, such as encountering a blank mask as the initial input after the first interaction. Second, we propose a novel Prompt Attention Learning Module (PALM) to mine useful prompt information in one interaction, enhancing the responsiveness of the network to user clicks. Last, we build a Time Series Information Propagation (TSIP) mechanism to extract the temporal relationships between multiple interactions and increase the model stability. Comparative experiments with other state-of-the-art (SOTA) medical image segmentation algorithms show that our method exhibits better segmentation accuracy and stability.

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arXiv2023

FFPN: Fourier Feature Pyramid Network for Ultrasound Image Segmentation

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.

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arXiv2023

RLIPv2: Fast Scaling of Relational Language-Image Pre-training

Relational Language-Image Pre-training (RLIP) aims to align vision representations with relational texts, thereby advancing the capability of relational reasoning in computer vision tasks. However, hindered by the slow convergence of RLIPv1 architecture and the limited availability of existing scene graph data, scaling RLIPv1 is challenging. In this paper, we propose RLIPv2, a fast converging model that enables the scaling of relational pre-training to large-scale pseudo-labelled scene graph data. To enable fast scaling, RLIPv2 introduces Asymmetric Language-Image Fusion (ALIF), a mechanism that facilitates earlier and deeper gated cross-modal fusion with sparsified language encoding layers. ALIF leads to comparable or better performance than RLIPv1 in a fraction of the time for pre-training and fine-tuning. To obtain scene graph data at scale, we extend object detection datasets with free-form relation labels by introducing a captioner (e.g., BLIP) and a designed Relation Tagger. The Relation Tagger assigns BLIP-generated relation texts to region pairs, thus enabling larger-scale relational pre-training. Through extensive experiments conducted on Human-Object Interaction Detection and Scene Graph Generation, RLIPv2 shows state-of-the-art performance on three benchmarks under fully-finetuning, few-shot and zero-shot settings. Notably, the largest RLIPv2 achieves 23.29mAP on HICO-DET without any fine-tuning, yields 32.22mAP with just 1% data and yields 45.09mAP with 100% data. Code and models are publicly available at https://github.com/JacobYuan7/RLIPv2.

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arXiv2023

OnUVS: Online Feature Decoupling Framework for High-Fidelity Ultrasound Video Synthesis

Ultrasound (US) imaging is indispensable in clinical practice. To diagnose certain diseases, sonographers must observe corresponding dynamic anatomic structures to gather comprehensive information. However, the limited availability of specific US video cases causes teaching difficulties in identifying corresponding diseases, which potentially impacts the detection rate of such cases. The synthesis of US videos may represent a promising solution to this issue. Nevertheless, it is challenging to accurately animate the intricate motion of dynamic anatomic structures while preserving image fidelity. To address this, we present a novel online feature-decoupling framework called OnUVS for high-fidelity US video synthesis. Our highlights can be summarized by four aspects. First, we introduced anatomic information into keypoint learning through a weakly-supervised training strategy, resulting in improved preservation of anatomical integrity and motion while minimizing the labeling burden. Second, to better preserve the integrity and textural information of US images, we implemented a dual-decoder that decouples the content and textural features in the generator. Third, we adopted a multiple-feature discriminator to extract a comprehensive range of visual cues, thereby enhancing the sharpness and fine details of the generated videos. Fourth, we constrained the motion trajectories of keypoints during online learning to enhance the fluidity of generated videos. Our validation and user studies on in-house echocardiographic and pelvic floor US videos showed that OnUVS synthesizes US videos with high fidelity.

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arXiv2023

GSMorph: Gradient Surgery for cine-MRI Cardiac Deformable Registration

Deep learning-based deformable registration methods have been widely investigated in diverse medical applications. Learning-based deformable registration relies on weighted objective functions trading off registration accuracy and smoothness of the deformation field. Therefore, they inevitably require tuning the hyperparameter for optimal registration performance. Tuning the hyperparameters is highly computationally expensive and introduces undesired dependencies on domain knowledge. In this study, we construct a registration model based on the gradient surgery mechanism, named GSMorph, to achieve a hyperparameter-free balance on multiple losses. In GSMorph, we reformulate the optimization procedure by projecting the gradient of similarity loss orthogonally to the plane associated with the smoothness constraint, rather than additionally introducing a hyperparameter to balance these two competing terms. Furthermore, our method is model-agnostic and can be merged into any deep registration network without introducing extra parameters or slowing down inference. In this study, We compared our method with state-of-the-art (SOTA) deformable registration approaches over two publicly available cardiac MRI datasets. GSMorph proves superior to five SOTA learning-based registration models and two conventional registration techniques, SyN and Demons, on both registration accuracy and smoothness.

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arXiv2023

Multi-IMU with Online Self-Consistency for Freehand 3D Ultrasound Reconstruction

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.

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arXiv2023

MUVF-YOLOX: A Multi-modal Ultrasound Video Fusion Network for Renal Tumor Diagnosis

Early diagnosis of renal cancer can greatly improve the survival rate of patients. Contrast-enhanced ultrasound (CEUS) is a cost-effective and non-invasive imaging technique and has become more and more frequently used for renal tumor diagnosis. However, the classification of benign and malignant renal tumors can still be very challenging due to the highly heterogeneous appearance of cancer and imaging artifacts. Our aim is to detect and classify renal tumors by integrating B-mode and CEUS-mode ultrasound videos. To this end, we propose a novel multi-modal ultrasound video fusion network that can effectively perform multi-modal feature fusion and video classification for renal tumor diagnosis. The attention-based multi-modal fusion module uses cross-attention and self-attention to extract modality-invariant features and modality-specific features in parallel. In addition, we design an object-level temporal aggregation (OTA) module that can automatically filter low-quality features and efficiently integrate temporal information from multiple frames to improve the accuracy of tumor diagnosis. Experimental results on a multicenter dataset show that the proposed framework outperforms the single-modal models and the competing methods. Furthermore, our OTA module achieves higher classification accuracy than the frame-level predictions. Our code is available at \url{https://github.com/JeunyuLi/MUAF}.

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arXiv2023

Inflated 3D Convolution-Transformer for Weakly-supervised Carotid Stenosis Grading with Ultrasound Videos

Localization of the narrowest position of the vessel and corresponding vessel and remnant vessel delineation in carotid ultrasound (US) are essential for carotid stenosis grading (CSG) in clinical practice. However, the pipeline is time-consuming and tough due to the ambiguous boundaries of plaque and temporal variation. To automatize this procedure, a large number of manual delineations are usually required, which is not only laborious but also not reliable given the annotation difficulty. In this study, we present the first video classification framework for automatic CSG. Our contribution is three-fold. First, to avoid the requirement of laborious and unreliable annotation, we propose a novel and effective video classification network for weakly-supervised CSG. Second, to ease the model training, we adopt an inflation strategy for the network, where pre-trained 2D convolution weights can be adapted into the 3D counterpart in our network for an effective warm start. Third, to enhance the feature discrimination of the video, we propose a novel attention-guided multi-dimension fusion (AMDF) transformer encoder to model and integrate global dependencies within and across spatial and temporal dimensions, where two lightweight cross-dimensional attention mechanisms are designed. Our approach is extensively validated on a large clinically collected carotid US video dataset, demonstrating state-of-the-art performance compared with strong competitors.

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arXiv2023

ModeT: Learning Deformable Image Registration via Motion Decomposition Transformer

The Transformer structures have been widely used in computer vision and have recently made an impact in the area of medical image registration. However, the use of Transformer in most registration networks is straightforward. These networks often merely use the attention mechanism to boost the feature learning as the segmentation networks do, but do not sufficiently design to be adapted for the registration task. In this paper, we propose a novel motion decomposition Transformer (ModeT) to explicitly model multiple motion modalities by fully exploiting the intrinsic capability of the Transformer structure for deformation estimation. The proposed ModeT naturally transforms the multi-head neighborhood attention relationship into the multi-coordinate relationship to model multiple motion modes. Then the competitive weighting module (CWM) fuses multiple deformation sub-fields to generate the resulting deformation field. Extensive experiments on two public brain magnetic resonance imaging (MRI) datasets show that our method outperforms current state-of-the-art registration networks and Transformers, demonstrating the potential of our ModeT for the challenging non-rigid deformation estimation problem. The benchmarks and our code are publicly available at https://github.com/ZAX130/SmileCode.

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