Jiong Wu

Jiong Wu, Yong Fan

Convolutional neural networks (CNNs) have been widely used to build deep learning models for medical image registration, but manually designed network architectures are not necessarily optimal. This paper presents a hierarchical NAS framework (HNAS-Reg), consisting of both convolutional operation search and network topology search, to identify the optimal network architecture for deformable medical image registration. To mitigate the computational overhead and memory constraints, a partial channel strategy is utilized without losing optimization quality. Experiments on three datasets, consisting of 636 T1-weighted magnetic resonance images (MRIs), have demonstrated that the proposal method can build a deep learning model with improved image registration accuracy and reduced model size, compared with state-of-the-art image registration approaches, including one representative traditional approach and two unsupervised learning-based approaches.

Jiong Wu, Kuang Gong

Deformable image registration plays an essential role in various medical image tasks. Existing deep learning-based deformable registration frameworks primarily utilize convolutional neural networks (CNNs) or Transformers to learn features to predict the deformations. However, the lack of semantic information in the learned features limits the registration performance. Furthermore, the similarity metric of the loss function is often evaluated only in the pixel space, which ignores the matching of high-level anatomical features and can lead to deformation folding. To address these issues, in this work, we proposed LDM-Morph, an unsupervised deformable registration algorithm for medical image registration. LDM-Morph integrated features extracted from the latent diffusion model (LDM) to enrich the semantic information. Additionally, a latent and global feature-based cross-attention module (LGCA) was designed to enhance the interaction of semantic information from LDM and global information from multi-head self-attention operations. Finally, a hierarchical metric was proposed to evaluate the similarity of image pairs in both the original pixel space and latent-feature space, enhancing topology preservation while improving registration accuracy. Extensive experiments on four public 2D cardiac image datasets show that the proposed LDM-Morph framework outperformed existing state-of-the-art CNNs- and Transformers-based registration methods regarding accuracy and topology preservation with comparable computational efficiency. Our code is publicly available at https://github.com/wujiong-hub/LDM-Morph.

Yang Xing, Jiong Wu, Yuheng Bu et al.

Although new vision foundation models such as Segment Anything Model 2 (SAM2) have significantly enhanced zero-shot image segmentation capabilities, reliance on human-provided prompts poses significant challenges in adapting SAM2 to medical image segmentation tasks. Moreover, SAM2's performance in medical image segmentation was limited by the domain shift issue, since it was originally trained on natural images and videos. To address these challenges, we proposed SAM2 with support-set guided prompting (SAM2-SGP), a framework that eliminated the need for manual prompts. The proposed model leveraged the memory mechanism of SAM2 to generate pseudo-masks using image-mask pairs from a support set via a Pseudo-mask Generation (PMG) module. We further introduced a novel Pseudo-mask Attention (PMA) module, which used these pseudo-masks to automatically generate bounding boxes and enhance localized feature extraction by guiding attention to relevant areas. Furthermore, a low-rank adaptation (LoRA) strategy was adopted to mitigate the domain shift issue. The proposed framework was evaluated on both 2D and 3D datasets across multiple medical imaging modalities, including fundus photography, X-ray, computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasound. The results demonstrated a significant performance improvement over state-of-the-art models, such as nnUNet and SwinUNet, as well as foundation models, such as SAM2 and MedSAM2, underscoring the effectiveness of the proposed approach. Our code is publicly available at https://github.com/astlian9/SAM_Support.

Jiong Wu, Yang Xing, Boxiao Yu et al.

Most publicly available medical segmentation datasets are only partially labeled, with annotations provided for a subset of anatomical structures. When multiple datasets are combined for training, this incomplete annotation poses challenges, as it limits the model's ability to learn shared anatomical representations among datasets. Furthermore, vision-only frameworks often fail to capture complex anatomical relationships and task-specific distinctions, leading to reduced segmentation accuracy and poor generalizability to unseen datasets. In this study, we proposed a novel CLIP-DINO Prompt-Driven Segmentation Network (CDPDNet), which combined a self-supervised vision transformer with CLIP-based text embedding and introduced task-specific text prompts to tackle these challenges. Specifically, the framework was constructed upon a convolutional neural network (CNN) and incorporated DINOv2 to extract both fine-grained and global visual features, which were then fused using a multi-head cross-attention module to overcome the limited long-range modeling capability of CNNs. In addition, CLIP-derived text embeddings were projected into the visual space to help model complex relationships among organs and tumors. To further address the partial label challenge and enhance inter-task discriminative capability, a Text-based Task Prompt Generation (TTPG) module that generated task-specific prompts was designed to guide the segmentation. Extensive experiments on multiple medical imaging datasets demonstrated that CDPDNet consistently outperformed existing state-of-the-art segmentation methods. Code and pretrained model are available at: https://github.com/wujiong-hub/CDPDNet.git.

Jiong Wu, Shuang Zhou, Li Lin et al.

Diffeomorphic image registration is a fundamental step in medical image analysis, owing to its capability to ensure the invertibility of transformations and preservation of topology. Currently, unsupervised learning-based registration techniques primarily extract features at the image level, potentially limiting their efficacy. This paper proposes a novel unsupervised learning-based fully convolutional network (FCN) framework for fast diffeomorphic image registration, emphasizing feature acquisition at the image patch level. Furthermore, a novel differential operator is introduced and integrated into the FCN architecture for parameter learning. Experiments are conducted on three distinct T1-weighted magnetic resonance imaging (T1w MRI) datasets. Comparative analyses with three state-of-the-art diffeomorphic image registration approaches including a typical conventional registration algorithm and two representative unsupervised learning-based methods, reveal that the proposed method exhibits superior performance in both registration accuracy and topology preservation.

Yang Xing, Jiong Wu, Savas Ozdemir et al.

Recent progress in medical vision-language models (VLMs) has achieved strong performance on image-level text-centric tasks such as report generation and visual question answering (VQA). However, achieving fine-grained visual grounding and volumetric spatial reasoning in 3D medical VLMs remains challenging, particularly when aiming to unify these capabilities within a single, generalizable framework. To address this challenge, we proposed MedVL-SAM2, a unified 3D medical multimodal model that concurrently supports report generation, VQA, and multi-paradigm segmentation, including semantic, referring, and interactive segmentation. MedVL-SAM2 integrates image-level reasoning and pixel-level perception through a cohesive architecture tailored for 3D medical imaging, and incorporates a SAM2-based volumetric segmentation module to enable precise multi-granular spatial reasoning. The model is trained in a multi-stage pipeline: it is first pre-trained on a large-scale corpus of 3D CT image-text pairs to align volumetric visual features with radiology-language embeddings. It is then jointly optimized with both language-understanding and segmentation objectives using a comprehensive 3D CT segmentation dataset. This joint training enables flexible interaction via language, point, or box prompts, thereby unifying high-level visual reasoning with spatially precise localization. Our unified architecture delivers state-of-the-art performance across report generation, VQA, and multiple 3D segmentation tasks. Extensive analyses further show that the model provides reliable 3D visual grounding, controllable interactive segmentation, and robust cross-modal reasoning, demonstrating that high-level semantic reasoning and precise 3D localization can be jointly achieved within a unified 3D medical VLM.

Li Lin, Zhonghua Wang, Jiewei Wu et al.

Optical coherence tomography angiography (OCTA) is a novel non-invasive imaging technique that allows visualizations of vasculature and foveal avascular zone (FAZ) across retinal layers. Clinical researches suggest that the morphology and contour irregularity of FAZ are important biomarkers of various ocular pathologies. Therefore, precise segmentation of FAZ has great clinical interest. Also, there is no existing research reporting that FAZ features can improve the performance of deep diagnostic classification networks. In this paper, we propose a novel multi-level boundary shape and distance aware joint learning framework, named BSDA-Net, for FAZ segmentation and diagnostic classification from OCTA images. Two auxiliary branches, namely boundary heatmap regression and signed distance map reconstruction branches, are constructed in addition to the segmentation branch to improve the segmentation performance, resulting in more accurate FAZ contours and fewer outliers. Moreover, both low-level and high-level features from the aforementioned three branches, including shape, size, boundary, and signed directional distance map of FAZ, are fused hierarchically with features from the diagnostic classifier. Through extensive experiments, the proposed BSDA-Net is found to yield state-of-the-art segmentation and classification results on the OCTA-500, OCTAGON, and FAZID datasets.

Jiong Wu, Xiaoying Tang

In this study, we proposed and validated a multi-atlas guided 3D fully convolutional network (FCN) ensemble model (M-FCN) for segmenting brain regions of interest (ROIs) from structural magnetic resonance images (MRIs). One major limitation of existing state-of-the-art 3D FCN segmentation models is that they often apply image patches of fixed size throughout training and testing, which may miss some complex tissue appearance patterns of different brain ROIs. To address this limitation, we trained a 3D FCN model for each ROI using patches of adaptive size and embedded outputs of the convolutional layers in the deconvolutional layers to further capture the local and global context patterns. In addition, with an introduction of multi-atlas based guidance in M-FCN, our segmentation was generated by combining the information of images and labels, which is highly robust. To reduce over-fitting of the FCN model on the training data, we adopted an ensemble strategy in the learning procedure. Evaluation was performed on two brain MRI datasets, aiming respectively at segmenting 14 subcortical and ventricular structures and 54 brain ROIs. The segmentation results of the proposed method were compared with those of a state-of-the-art multi-atlas based segmentation method and an existing 3D FCN segmentation model. Our results suggested that the proposed method had a superior segmentation performance.