Zhenrong Shen

Zhenrong Shen, Xi Ouyang, Bin Xiao et al.

Lung nodule detection in chest X-ray (CXR) images is common to early screening of lung cancers. Deep-learning-based Computer-Assisted Diagnosis (CAD) systems can support radiologists for nodule screening in CXR. However, it requires large-scale and diverse medical data with high-quality annotations to train such robust and accurate CADs. To alleviate the limited availability of such datasets, lung nodule synthesis methods are proposed for the sake of data augmentation. Nevertheless, previous methods lack the ability to generate nodules that are realistic with the size attribute desired by the detector. To address this issue, we introduce a novel lung nodule synthesis framework in this paper, which decomposes nodule attributes into three main aspects including shape, size, and texture, respectively. A GAN-based Shape Generator firstly models nodule shapes by generating diverse shape masks. The following Size Modulation then enables quantitative control on the diameters of the generated nodule shapes in pixel-level granularity. A coarse-to-fine gated convolutional Texture Generator finally synthesizes visually plausible nodule textures conditioned on the modulated shape masks. Moreover, we propose to synthesize nodule CXR images by controlling the disentangled nodule attributes for data augmentation, in order to better compensate for the nodules that are easily missed in the detection task. Our experiments demonstrate the enhanced image quality, diversity, and controllability of the proposed lung nodule synthesis framework. We also validate the effectiveness of our data augmentation on greatly improving nodule detection performance.

Yichi Zhang, Zhenrong Shen

The unprecedented developments in segmentation foundational models have become a dominant force in the field of computer vision, introducing a multitude of previously unexplored capabilities in a wide range of natural images and videos. Specifically, the Segment Anything Model (SAM) signifies a noteworthy expansion of the prompt-driven paradigm into the domain of image segmentation. The recent introduction of SAM2 effectively extends the original SAM to a streaming fashion and demonstrates strong performance in video segmentation. However, due to the substantial distinctions between natural and medical images, the effectiveness of these models on biomedical images and videos is still under exploration. This paper presents an overview of recent efforts in applying and adapting SAM2 to biomedical images and videos. The findings indicate that while SAM2 shows promise in reducing annotation burdens and enabling zero-shot segmentation, its performance varies across different datasets and tasks. Addressing the domain gap between natural and medical images through adaptation and fine-tuning is essential to fully unleash SAM2's potential in clinical applications. To support ongoing research endeavors, we maintain an active repository that contains up-to-date SAM & SAM2-related papers and projects at https://github.com/YichiZhang98/SAM4MIS.

Yitao Zhu, Zhenrong Shen, Zihao Zhao et al.

The common practice in developing computer-aided diagnosis (CAD) models based on transformer architectures usually involves fine-tuning from ImageNet pre-trained weights. However, with recent advances in large-scale pre-training and the practice of scaling laws, Vision Transformers (ViT) have become much larger and less accessible to medical imaging communities. Additionally, in real-world scenarios, the deployments of multiple CAD models can be troublesome due to problems such as limited storage space and time-consuming model switching. To address these challenges, we propose a new method MeLo (Medical image Low-rank adaptation), which enables the development of a single CAD model for multiple clinical tasks in a lightweight manner. It adopts low-rank adaptation instead of resource-demanding fine-tuning. By fixing the weight of ViT models and only adding small low-rank plug-ins, we achieve competitive results on various diagnosis tasks across different imaging modalities using only a few trainable parameters. Specifically, our proposed method achieves comparable performance to fully fine-tuned ViT models on four distinct medical imaging datasets using about 0.17% trainable parameters. Moreover, MeLo adds only about 0.5MB of storage space and allows for extremely fast model switching in deployment and inference. Our source code and pre-trained weights are available on our website (https://absterzhu.github.io/melo.github.io/).

Yichi Zhang, Zhenrong Shen, Rushi Jiao

Due to the inherent flexibility of prompting, foundation models have emerged as the predominant force in the fields of natural language processing and computer vision. The recent introduction of the Segment Anything Model (SAM) signifies a noteworthy expansion of the prompt-driven paradigm into the domain of image segmentation, thereby introducing a plethora of previously unexplored capabilities. However, the viability of its application to medical image segmentation remains uncertain, given the substantial distinctions between natural and medical images. In this work, we provide a comprehensive overview of recent endeavors aimed at extending the efficacy of SAM to medical image segmentation tasks, encompassing both empirical benchmarking and methodological adaptations. Additionally, we explore potential avenues for future research directions in SAM's role within medical image segmentation. While direct application of SAM to medical image segmentation does not yield satisfactory performance on multi-modal and multi-target medical datasets so far, numerous insights gleaned from these efforts serve as valuable guidance for shaping the trajectory of foundational models in the realm of medical image analysis. To support ongoing research endeavors, we maintain an active repository that contains an up-to-date paper list and a succinct summary of open-source projects at https://github.com/YichiZhang98/SAM4MIS.

Zhenrong Shen, Maosong Cao, Sheng Wang et al.

Automatic examination of thin-prep cytologic test (TCT) slides can assist pathologists in finding cervical abnormality for accurate and efficient cancer screening. Current solutions mostly need to localize suspicious cells and classify abnormality based on local patches, concerning the fact that whole slide images of TCT are extremely large. It thus requires many annotations of normal and abnormal cervical cells, to supervise the training of the patch-level classifier for promising performance. In this paper, we propose CellGAN to synthesize cytopathological images of various cervical cell types for augmenting patch-level cell classification. Built upon a lightweight backbone, CellGAN is equipped with a non-linear class mapping network to effectively incorporate cell type information into image generation. We also propose the Skip-layer Global Context module to model the complex spatial relationship of the cells, and attain high fidelity of the synthesized images through adversarial learning. Our experiments demonstrate that CellGAN can produce visually plausible TCT cytopathological images for different cell types. We also validate the effectiveness of using CellGAN to greatly augment patch-level cell classification performance.

Xin Wang, Sheng Wang, Honglin Xiong et al.

Magnetic resonance (MR) images collected in 2D clinical protocols typically have large inter-slice spacing, resulting in high in-plane resolution and reduced through-plane resolution. Super-resolution technique can enhance the through-plane resolution of MR images to facilitate downstream visualization and computer-aided diagnosis. However, most existing works train the super-resolution network at a fixed scaling factor, which is not friendly to clinical scenes of varying inter-slice spacing in MR scanning. Inspired by the recent progress in implicit neural representation, we propose a Spatial Attention-based Implicit Neural Representation (SA-INR) network for arbitrary reduction of MR inter-slice spacing. The SA-INR aims to represent an MR image as a continuous implicit function of 3D coordinates. In this way, the SA-INR can reconstruct the MR image with arbitrary inter-slice spacing by continuously sampling the coordinates in 3D space. In particular, a local-aware spatial attention operation is introduced to model nearby voxels and their affinity more accurately in a larger receptive field. Meanwhile, to improve the computational efficiency, a gradient-guided gating mask is proposed for applying the local-aware spatial attention to selected areas only. We evaluate our method on the public HCP-1200 dataset and the clinical knee MR dataset to demonstrate its superiority over other existing methods.

Xin Wang, Zhenrong Shen, Zhiyun Song et al.

Magnetic resonance (MR) images collected in 2D scanning protocols typically have large inter-slice spacing, resulting in high in-plane resolution but reduced through-plane resolution. Super-resolution techniques can reduce the inter-slice spacing of 2D scanned MR images, facilitating the downstream visual experience and computer-aided diagnosis. However, most existing super-resolution methods are trained at a fixed scaling ratio, which is inconvenient in clinical settings where MR scanning may have varying inter-slice spacings. To solve this issue, we propose Hierarchical Feature Conditional Diffusion (HiFi-Diff)} for arbitrary reduction of MR inter-slice spacing. Given two adjacent MR slices and the relative positional offset, HiFi-Diff can iteratively convert a Gaussian noise map into any desired in-between MR slice. Furthermore, to enable fine-grained conditioning, the Hierarchical Feature Extraction (HiFE) module is proposed to hierarchically extract conditional features and conduct element-wise modulation. Our experimental results on the publicly available HCP-1200 dataset demonstrate the high-fidelity super-resolution capability of HiFi-Diff and its efficacy in enhancing downstream segmentation performance.

Zhiyun Song, Zengxin Qi, Xin Wang et al.

Cross-modality synthesis (CMS), super-resolution (SR), and their combination (CMSR) have been extensively studied for magnetic resonance imaging (MRI). Their primary goals are to enhance the imaging quality by synthesizing the desired modality and reducing the slice thickness. Despite the promising synthetic results, these techniques are often tailored to specific tasks, thereby limiting their adaptability to complex clinical scenarios. Therefore, it is crucial to build a unified network that can handle various image synthesis tasks with arbitrary requirements of modality and resolution settings, so that the resources for training and deploying the models can be greatly reduced. However, none of the previous works is capable of performing CMS, SR, and CMSR using a unified network. Moreover, these MRI reconstruction methods often treat alias frequencies improperly, resulting in suboptimal detail restoration. In this paper, we propose a Unified Co-Modulated Alias-free framework (Uni-COAL) to accomplish the aforementioned tasks with a single network. The co-modulation design of the image-conditioned and stochastic attribute representations ensures the consistency between CMS and SR, while simultaneously accommodating arbitrary combinations of input/output modalities and thickness. The generator of Uni-COAL is also designed to be alias-free based on the Shannon-Nyquist signal processing framework, ensuring effective suppression of alias frequencies. Additionally, we leverage the semantic prior of Segment Anything Model (SAM) to guide Uni-COAL, ensuring a more authentic preservation of anatomical structures during synthesis. Experiments on three datasets demonstrate that Uni-COAL outperforms the alternatives in CMS, SR, and CMSR tasks for MR images, which highlights its generalizability to wide-range applications.

Xiangyu Zhao, Di Zang, Sheng Wang et al.

Brain network analysis for traumatic brain injury (TBI) patients is critical for its consciousness level assessment and prognosis evaluation, which requires the segmentation of certain consciousness-related brain regions. However, it is difficult to construct a TBI segmentation model as manually annotated MR scans of TBI patients are hard to collect. Data augmentation techniques can be applied to alleviate the issue of data scarcity. However, conventional data augmentation strategies such as spatial and intensity transformation are unable to mimic the deformation and lesions in traumatic brains, which limits the performance of the subsequent segmentation task. To address these issues, we propose a novel medical image inpainting model named TBI-GAN to synthesize TBI MR scans with paired brain label maps. The main strength of our TBI-GAN method is that it can generate TBI images and corresponding label maps simultaneously, which has not been achieved in the previous inpainting methods for medical images. We first generate the inpainted image under the guidance of edge information following a coarse-to-fine manner, and then the synthesized intensity image is used as the prior for label inpainting. Furthermore, we introduce a registration-based template augmentation pipeline to increase the diversity of the synthesized image pairs and enhance the capacity of data augmentation. Experimental results show that the proposed TBI-GAN method can produce sufficient synthesized TBI images with high quality and valid label maps, which can greatly improve the 2D and 3D traumatic brain segmentation performance compared with the alternatives.

Jiangdong Cai, Yan Chen, Zhenrong Shen et al.

In digital pathology, acquiring all-in-focus images is essential to high-quality imaging and high-efficient clinical workflow. Traditional scanners achieve this by scanning at multiple focal planes of varying depths and then merging them, which is relatively slow and often struggles with complex tissue defocus. Recent prevailing image restoration technique provides a means to restore high-quality pathology images from scans of single focal planes. However, existing image restoration methods are inadequate, due to intricate defocus patterns in pathology images and their domain-specific semantic complexities. In this work, we devise a two-stage restoration solution cascading a transformer and a diffusion model, to benefit from their powers in preserving image fidelity and perceptual quality, respectively. We particularly propose a novel mixture of prompts for the two-stage solution. Given initial prompt that models defocus in microscopic imaging, we design two prompts that describe the high-level image semantics from pathology foundation model and the fine-grained tissue structures via edge extraction. We demonstrate that, by feeding the prompt mixture to our method, we can restore high-quality pathology images from single-focal-plane scans, implying high potentials of the mixture of prompts to clinical usage. Code will be publicly available at https://github.com/caijd2000/MoP.

Yitao Zhu, Yuan Yin, Zhenrong Shen et al.

The growing complexity and scale of visual model pre-training have made developing and deploying multi-task computer-aided diagnosis (CAD) systems increasingly challenging and resource-intensive. Furthermore, the medical imaging community lacks an open-source CAD platform to enable the rapid creation of efficient and extendable diagnostic models. To address these issues, we propose UniCAD, a unified architecture that leverages the robust capabilities of pre-trained vision foundation models to seamlessly handle both 2D and 3D medical images while requiring only minimal task-specific parameters. UniCAD introduces two key innovations: (1) Efficiency: A low-rank adaptation strategy is employed to adapt a pre-trained visual model to the medical image domain, achieving performance on par with fully fine-tuned counterparts while introducing only 0.17% trainable parameters. (2) Plug-and-Play: A modular architecture that combines a frozen foundation model with multiple plug-and-play experts, enabling diverse tasks and seamless functionality expansion. Building on this unified CAD architecture, we establish an open-source platform where researchers can share and access lightweight CAD experts, fostering a more equitable and efficient research ecosystem. Comprehensive experiments across 12 diverse medical datasets demonstrate that UniCAD consistently outperforms existing methods in both accuracy and deployment efficiency. The source code and project page are available at https://mii-laboratory.github.io/UniCAD/.

Jiangdong Cai, Haotian Jiang, Zhenrong Shen et al.

The deployment of computer-aided diagnosis systems for cervical cancer screening using whole slide images (WSIs) faces critical challenges due to domain shifts caused by staining variations across different scanners and imaging environments. While existing stain augmentation methods improve patch-level robustness, they fail to scale to WSIs due to two key limitations: (1) inconsistent stain patterns when extending patch operations to gigapixel slides, and (2) prohibitive computational/storage costs from offline processing of augmented WSIs.To address this, we propose Latent Style Augmentation (LSA), a framework that performs efficient, online stain augmentation directly on WSI-level latent features. We first introduce WSAug, a WSI-level stain augmentation method ensuring consistent stain across patches within a WSI. Using offline-augmented WSIs by WSAug, we design and train Stain Transformer, which can simulate targeted style in the latent space, efficiently enhancing the robustness of the WSI-level classifier. We validate our method on a multi-scanner WSI dataset for cervical cancer diagnosis. Despite being trained on data from a single scanner, our approach achieves significant performance improvements on out-of-distribution data from other scanners. Code will be available at https://github.com/caijd2000/LSA.

Xiangyu Zhao, Sheng Wang, Zhiyun Song et al.

Accurate automatic segmentation of medical images typically requires large datasets with high-quality annotations, making it less applicable in clinical settings due to limited training data. One-shot segmentation based on learned transformations (OSSLT) has shown promise when labeled data is extremely limited, typically including unsupervised deformable registration, data augmentation with learned registration, and segmentation learned from augmented data. However, current one-shot segmentation methods are challenged by limited data diversity during augmentation, and potential label errors caused by imperfect registration. To address these issues, we propose a novel one-shot medical image segmentation method with adversarial training and label error rectification (AdLER), with the aim of improving the diversity of generated data and correcting label errors to enhance segmentation performance. Specifically, we implement a novel dual consistency constraint to ensure anatomy-aligned registration that lessens registration errors. Furthermore, we develop an adversarial training strategy to augment the atlas image, which ensures both generation diversity and segmentation robustness. We also propose to rectify potential label errors in the augmented atlas images by estimating segmentation uncertainty, which can compensate for the imperfect nature of deformable registration and improve segmentation authenticity. Experiments on the CANDI and ABIDE datasets demonstrate that the proposed AdLER outperforms previous state-of-the-art methods by 0.7% (CANDI), 3.6% (ABIDE "seen"), and 4.9% (ABIDE "unseen") in segmentation based on Dice scores, respectively. The source code will be available at https://github.com/hsiangyuzhao/AdLER.

Yan Kong, Sheng Wang, Jiangdong Cai et al.

Accurate detection of vulvovaginal candidiasis is critical for women's health, yet its sparse distribution and visually ambiguous characteristics pose significant challenges for accurate identification by pathologists and neural networks alike. Our eye-tracking data reveals that areas garnering sustained attention - yet not marked by experts after deliberation - are often aligned with false positives of neural networks. Leveraging this finding, we introduce Gaze-DETR, a pioneering method that integrates gaze data to enhance neural network precision by diminishing false positives. Gaze-DETR incorporates a universal gaze-guided warm-up protocol applicable across various detection methods and a gaze-guided rectification strategy specifically designed for DETR-based models. Our comprehensive tests confirm that Gaze-DETR surpasses existing leading methods, showcasing remarkable improvements in detection accuracy and generalizability.

Mengjie Xu, Yitao Zhu, Haotian Jiang et al.

Multi-view object tracking (MVOT) offers promising solutions to challenges such as occlusion and target loss, which are common in traditional single-view tracking. However, progress has been limited by the lack of comprehensive multi-view datasets and effective cross-view integration methods. To overcome these limitations, we compiled a Multi-View object Tracking (MVTrack) dataset of 234K high-quality annotated frames featuring 27 distinct objects across various scenes. In conjunction with this dataset, we introduce a novel MVOT method, Multi-View Integration Tracker (MITracker), to efficiently integrate multi-view object features and provide stable tracking outcomes. MITracker can track any object in video frames of arbitrary length from arbitrary viewpoints. The key advancements of our method over traditional single-view approaches come from two aspects: (1) MITracker transforms 2D image features into a 3D feature volume and compresses it into a bird's eye view (BEV) plane, facilitating inter-view information fusion; (2) we propose an attention mechanism that leverages geometric information from fused 3D feature volume to refine the tracking results at each view. MITracker outperforms existing methods on the MVTrack and GMTD datasets, achieving state-of-the-art performance. The code and the new dataset will be available at https://mii-laboratory.github.io/MITracker/.

Zhenrong Shen, Manman Fei, Xin Wang et al.

Automatic thin-prep cytologic test (TCT) screening can assist pathologists in finding cervical abnormality towards accurate and efficient cervical cancer diagnosis. Current automatic TCT screening systems mostly involve abnormal cervical cell detection, which generally requires large-scale and diverse training data with high-quality annotations to achieve promising performance. Pathological image synthesis is naturally raised to minimize the efforts in data collection and annotation. However, it is challenging to generate realistic large-size cytopathological images while simultaneously synthesizing visually plausible appearances for small-size abnormal cervical cells. In this paper, we propose a two-stage image synthesis framework to create synthetic data for augmenting cervical abnormality screening. In the first Global Image Generation stage, a Normal Image Generator is designed to generate cytopathological images full of normal cervical cells. In the second Local Cell Editing stage, normal cells are randomly selected from the generated images and then are converted to different types of abnormal cells using the proposed Abnormal Cell Synthesizer. Both Normal Image Generator and Abnormal Cell Synthesizer are built upon Stable Diffusion, a pre-trained foundation model for image synthesis, via parameter-efficient fine-tuning methods for customizing cytopathological image contents and extending spatial layout controllability, respectively. Our experiments demonstrate the synthetic image quality, diversity, and controllability of the proposed synthesis framework, and validate its data augmentation effectiveness in enhancing the performance of abnormal cervical cell detection.

Jiaxu Zheng, Zhenrong Shen, Lichi Zhang et al.

Deep-learning-based MR-to-CT synthesis can estimate the electron density of tissues, thereby facilitating PET attenuation correction in whole-body PET/MR imaging. However, whole-body MR-to-CT synthesis faces several challenges including the issue of spatial misalignment and the complexity of intensity mapping, primarily due to the variety of tissues and organs throughout the whole body. Here we propose a novel whole-body MR-to-CT synthesis framework, which consists of three novel modules to tackle these challenges: (1) Structure-Guided Synthesis module leverages structure-guided attention gates to enhance synthetic image quality by diminishing unnecessary contours of soft tissues; (2) Spatial Alignment module yields precise registration between paired MR and CT images by taking into account the impacts of tissue volumes and respiratory movements, thus providing well-aligned ground-truth CT images during training; (3) Semantic Alignment module utilizes contrastive learning to constrain organ-related semantic information, thereby ensuring the semantic authenticity of synthetic CT images.We conduct extensive experiments to demonstrate that the proposed whole-body MR-to-CT framework can produce visually plausible and semantically realistic CT images, and validate its utility in PET attenuation correction.