Bo Zhou

Bo Zhou, Jo Schlemper, Neel Dey et al. · mit

While enabling accelerated acquisition and improved reconstruction accuracy, current deep MRI reconstruction networks are typically supervised, require fully sampled data, and are limited to Cartesian sampling patterns. These factors limit their practical adoption as fully-sampled MRI is prohibitively time-consuming to acquire clinically. Further, non-Cartesian sampling patterns are particularly desirable as they are more amenable to acceleration and show improved motion robustness. To this end, we present a fully self-supervised approach for accelerated non-Cartesian MRI reconstruction which leverages self-supervision in both k-space and image domains. In training, the undersampled data are split into disjoint k-space domain partitions. For the k-space self-supervision, we train a network to reconstruct the input undersampled data from both the disjoint partitions and from itself. For the image-level self-supervision, we enforce appearance consistency obtained from the original undersampled data and the two partitions. Experimental results on our simulated multi-coil non-Cartesian MRI dataset demonstrate that DDSS can generate high-quality reconstruction that approaches the accuracy of the fully supervised reconstruction, outperforming previous baseline methods. Finally, DDSS is shown to scale to highly challenging real-world clinical MRI reconstruction acquired on a portable low-field (0.064 T) MRI scanner with no data available for supervised training while demonstrating improved image quality as compared to traditional reconstruction, as determined by a radiologist study.

Jieneng Chen, Yingda Xia, Jiawen Yao et al.

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (CancerUniT) model to jointly detect tumor existence & location and diagnose tumor characteristics for eight major cancers in CT scans. CancerUniT is a query-based Mask Transformer model with the output of multi-tumor prediction. We decouple the object queries into organ queries, tumor detection queries and tumor diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. CancerUniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, CancerUniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-disease methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. This moves one step closer towards a universal high performance cancer screening tool.

Xiongchao Chen, Bo Zhou, Huidong Xie et al.

Single-photon emission computed tomography (SPECT) is a widely applied imaging approach for diagnosis of coronary artery diseases. Attenuation maps (u-maps) derived from computed tomography (CT) are utilized for attenuation correction (AC) to improve diagnostic accuracy of cardiac SPECT. However, SPECT and CT are obtained sequentially in clinical practice, which potentially induces misregistration between the two scans. Convolutional neural networks (CNN) are powerful tools for medical image registration. Previous CNN-based methods for cross-modality registration either directly concatenated two input modalities as an early feature fusion or extracted image features using two separate CNN modules for a late fusion. These methods do not fully extract or fuse the cross-modality information. Besides, deep-learning-based rigid registration of cardiac SPECT and CT-derived u-maps has not been investigated before. In this paper, we propose a Dual-Branch Squeeze-Fusion-Excitation (DuSFE) module for the registration of cardiac SPECT and CT-derived u-maps. DuSFE fuses the knowledge from multiple modalities to recalibrate both channel-wise and spatial features for each modality. DuSFE can be embedded at multiple convolutional layers to enable feature fusion at different spatial dimensions. Our studies using clinical data demonstrated that a network embedded with DuSFE generated substantial lower registration errors and therefore more accurate AC SPECT images than previous methods.

Kundan Sai Prabhu Thota, Sungho Suh, Bo Zhou et al.

The estimation of 3D human body shape and clothing measurements is crucial for virtual try-on and size recommendation problems in the fashion industry but has always been a challenging problem due to several conditions, such as lack of publicly available realistic datasets, ambiguity in multiple camera resolutions, and the undefinable human shape space. Existing works proposed various solutions to these problems but could not succeed in the industry adaptation because of complexity and restrictions. To solve the complexity and challenges, in this paper, we propose a simple yet effective architecture to estimate both shape and measures from frontal- and side-view images. We utilize silhouette segmentation from the two multi-view images and implement an auto-encoder network to learn low-dimensional features from segmented silhouettes. Then, we adopt a kernel-based regularized regression module to estimate the body shape and measurements. The experimental results show that the proposed method provides competitive results on the synthetic dataset, NOMO-3d-400-scans Dataset, and RGB Images of humans captured in different cameras.

Bo Zhou, Yingda Xia, Jiawen Yao et al.

Pancreatic cancer is one of the leading causes of cancer-related death. Accurate detection, segmentation, and differential diagnosis of the full taxonomy of pancreatic lesions, i.e., normal, seven major types of lesions, and other lesions, is critical to aid the clinical decision-making of patient management and treatment. However, existing works focus on segmentation and classification for very specific lesion types (PDAC) or groups. Moreover, none of the previous work considers using lesion prevalence-related non-imaging patient information to assist the differential diagnosis. To this end, we develop a meta-information-aware dual-path transformer and exploit the feasibility of classification and segmentation of the full taxonomy of pancreatic lesions. Specifically, the proposed method consists of a CNN-based segmentation path (S-path) and a transformer-based classification path (C-path). The S-path focuses on initial feature extraction by semantic segmentation using a UNet-based network. The C-path utilizes both the extracted features and meta-information for patient-level classification based on stacks of dual-path transformer blocks that enhance the modeling of global contextual information. A large-scale multi-phase CT dataset of 3,096 patients with pathology-confirmed pancreatic lesion class labels, voxel-wise manual annotations of lesions from radiologists, and patient meta-information, was collected for training and evaluations. Our results show that our method can enable accurate classification and segmentation of the full taxonomy of pancreatic lesions, approaching the accuracy of the radiologist's report and significantly outperforming previous baselines. Results also show that adding the common meta-information, i.e., gender and age, can boost the model's performance, thus demonstrating the importance of meta-information for aiding pancreatic disease diagnosis.

Bo Zhou, Yu-Jung Tsai, Jiazhen Zhang et al.

Patient motion during PET is inevitable. Its long acquisition time not only increases the motion and the associated artifacts but also the patient's discomfort, thus PET acceleration is desirable. However, accelerating PET acquisition will result in reconstructed images with low SNR, and the image quality will still be degraded by motion-induced artifacts. Most of the previous PET motion correction methods are motion type specific that require motion modeling, thus may fail when multiple types of motion present together. Also, those methods are customized for standard long acquisition and could not be directly applied to accelerated PET. To this end, modeling-free universal motion correction reconstruction for accelerated PET is still highly under-explored. In this work, we propose a novel deep learning-aided motion correction and reconstruction framework for accelerated PET, called Fast-MC-PET. Our framework consists of a universal motion correction (UMC) and a short-to-long acquisition reconstruction (SL-Reon) module. The UMC enables modeling-free motion correction by estimating quasi-continuous motion from ultra-short frame reconstructions and using this information for motion-compensated reconstruction. Then, the SL-Recon converts the accelerated UMC image with low counts to a high-quality image with high counts for our final reconstruction output. Our experimental results on human studies show that our Fast-MC-PET can enable 7-fold acceleration and use only 2 minutes acquisition to generate high-quality reconstruction images that outperform/match previous motion correction reconstruction methods using standard 15 minutes long acquisition data.

Bo Zhou, Huidong Xie, Qiong Liu et al.

Low-count PET is an efficient way to reduce radiation exposure and acquisition time, but the reconstructed images often suffer from low signal-to-noise ratio (SNR), thus affecting diagnosis and other downstream tasks. Recent advances in deep learning have shown great potential in improving low-count PET image quality, but acquiring a large, centralized, and diverse dataset from multiple institutions for training a robust model is difficult due to privacy and security concerns of patient data. Moreover, low-count PET data at different institutions may have different data distribution, thus requiring personalized models. While previous federated learning (FL) algorithms enable multi-institution collaborative training without the need of aggregating local data, addressing the large domain shift in the application of multi-institutional low-count PET denoising remains a challenge and is still highly under-explored. In this work, we propose FedFTN, a personalized federated learning strategy that addresses these challenges. FedFTN uses a local deep feature transformation network (FTN) to modulate the feature outputs of a globally shared denoising network, enabling personalized low-count PET denoising for each institution. During the federated learning process, only the denoising network's weights are communicated and aggregated, while the FTN remains at the local institutions for feature transformation. We evaluated our method using a large-scale dataset of multi-institutional low-count PET imaging data from three medical centers located across three continents, and showed that FedFTN provides high-quality low-count PET images, outperforming previous baseline FL reconstruction methods across all low-count levels at all three institutions.

Xiongchao Chen, Bo Zhou, Xueqi Guo et al.

Single-Photon Emission Computed Tomography (SPECT) is widely applied for the diagnosis of coronary artery diseases. Low-dose (LD) SPECT aims to minimize radiation exposure but leads to increased image noise. Limited-view (LV) SPECT, such as the latest GE MyoSPECT ES system, enables accelerated scanning and reduces hardware expenses but degrades reconstruction accuracy. Additionally, Computed Tomography (CT) is commonly used to derive attenuation maps ($μ$-maps) for attenuation correction (AC) of cardiac SPECT, but it will introduce additional radiation exposure and SPECT-CT misalignments. Although various methods have been developed to solely focus on LD denoising, LV reconstruction, or CT-free AC in SPECT, the solution for simultaneously addressing these tasks remains challenging and under-explored. Furthermore, it is essential to explore the potential of fusing cross-domain and cross-modality information across these interrelated tasks to further enhance the accuracy of each task. Thus, we propose a Dual-Domain Coarse-to-Fine Progressive Network (DuDoCFNet), a multi-task learning method for simultaneous LD denoising, LV reconstruction, and CT-free $μ$-map generation of cardiac SPECT. Paired dual-domain networks in DuDoCFNet are cascaded using a multi-layer fusion mechanism for cross-domain and cross-modality feature fusion. Two-stage progressive learning strategies are applied in both projection and image domains to achieve coarse-to-fine estimations of SPECT projections and CT-derived $μ$-maps. Our experiments demonstrate DuDoCFNet's superior accuracy in estimating projections, generating $μ$-maps, and AC reconstructions compared to existing single- or multi-task learning methods, under various iterations and LD levels. The source code of this work is available at https://github.com/XiongchaoChen/DuDoCFNet-MultiTask.

Yinchi Zhou, Huidong Xie, Menghua Xia et al.

Low-count positron emission tomography (LCPET) imaging can reduce patients' exposure to radiation but often suffers from increased image noise and reduced lesion detectability, necessitating effective denoising techniques. Diffusion models have shown promise in LCPET denoising for recovering degraded image quality. However, training such models requires large and diverse datasets, which are challenging to obtain in the medical domain. To address data scarcity and privacy concerns, we combine diffusion models with federated learning -- a decentralized training approach where models are trained individually at different sites, and their parameters are aggregated on a central server over multiple iterations. The variation in scanner types and image noise levels within and across institutions poses additional challenges for federated learning in LCPET denoising. In this study, we propose a novel noise-embedded federated learning diffusion model (Fed-NDIF) to address these challenges, leveraging a multicenter dataset and varying count levels. Our approach incorporates liver normalized standard deviation (NSTD) noise embedding into a 2.5D diffusion model and utilizes the Federated Averaging (FedAvg) algorithm to aggregate locally trained models into a global model, which is subsequently fine-tuned on local datasets to optimize performance and obtain personalized models. Extensive validation on datasets from the University of Bern, Ruijin Hospital in Shanghai, and Yale-New Haven Hospital demonstrates the superior performance of our method in enhancing image quality and improving lesion quantification. The Fed-NDIF model shows significant improvements in PSNR, SSIM, and NMSE of the entire 3D volume, as well as enhanced lesion detectability and quantification, compared to local diffusion models and federated UNet-based models.

Yicheng Gao, Jinkui Hao, Bo Zhou

Recent advancements in deep learning have shown transformative potential in medical imaging, yet concerns about fairness persist due to performance disparities across demographic subgroups. Existing methods aim to address these biases by mitigating sensitive attributes in image data; however, these attributes often carry clinically relevant information, and their removal can compromise model performance-a highly undesirable outcome. To address this challenge, we propose Fair Re-fusion After Disentanglement (FairREAD), a novel, simple, and efficient framework that mitigates unfairness by re-integrating sensitive demographic attributes into fair image representations. FairREAD employs orthogonality constraints and adversarial training to disentangle demographic information while using a controlled re-fusion mechanism to preserve clinically relevant details. Additionally, subgroup-specific threshold adjustments ensure equitable performance across demographic groups. Comprehensive evaluations on a large-scale clinical X-ray dataset demonstrate that FairREAD significantly reduces unfairness metrics while maintaining diagnostic accuracy, establishing a new benchmark for fairness and performance in medical image classification.

Tianqi Chen, Jun Hou, Yinchi Zhou et al.

Positron Emission Tomography (PET) is an important clinical imaging tool but inevitably introduces radiation hazards to patients and healthcare providers. Reducing the tracer injection dose and eliminating the CT acquisition for attenuation correction can reduce the overall radiation dose, but often results in PET with high noise and bias. Thus, it is desirable to develop 3D methods to translate the non-attenuation-corrected low-dose PET (NAC-LDPET) into attenuation-corrected standard-dose PET (AC-SDPET). Recently, diffusion models have emerged as a new state-of-the-art deep learning method for image-to-image translation, better than traditional CNN-based methods. However, due to the high computation cost and memory burden, it is largely limited to 2D applications. To address these challenges, we developed a novel 2.5D Multi-view Averaging Diffusion Model (MADM) for 3D image-to-image translation with application on NAC-LDPET to AC-SDPET translation. Specifically, MADM employs separate diffusion models for axial, coronal, and sagittal views, whose outputs are averaged in each sampling step to ensure the 3D generation quality from multiple views. To accelerate the 3D sampling process, we also proposed a strategy to use the CNN-based 3D generation as a prior for the diffusion model. Our experimental results on human patient studies suggested that MADM can generate high-quality 3D translation images, outperforming previous CNN-based and Diffusion-based baseline methods.

Bo Zhou, Jun Hou, Tianqi Chen et al.

Low-dose PET offers a valuable means of minimizing radiation exposure in PET imaging. However, the prevalent practice of employing additional CT scans for generating attenuation maps (u-map) for PET attenuation correction significantly elevates radiation doses. To address this concern and further mitigate radiation exposure in low-dose PET exams, we propose POUR-Net - an innovative population-prior-aided over-under-representation network that aims for high-quality attenuation map generation from low-dose PET. First, POUR-Net incorporates an over-under-representation network (OUR-Net) to facilitate efficient feature extraction, encompassing both low-resolution abstracted and fine-detail features, for assisting deep generation on the full-resolution level. Second, complementing OUR-Net, a population prior generation machine (PPGM) utilizing a comprehensive CT-derived u-map dataset, provides additional prior information to aid OUR-Net generation. The integration of OUR-Net and PPGM within a cascade framework enables iterative refinement of $μ$-map generation, resulting in the production of high-quality $μ$-maps. Experimental results underscore the effectiveness of POUR-Net, showing it as a promising solution for accurate CT-free low-count PET attenuation correction, which also surpasses the performance of previous baseline methods.

Bo Zhou, Neel Dey, Jo Schlemper et al.

Multi-contrast MRI (MC-MRI) captures multiple complementary imaging modalities to aid in radiological decision-making. Given the need for lowering the time cost of multiple acquisitions, current deep accelerated MRI reconstruction networks focus on exploiting the redundancy between multiple contrasts. However, existing works are largely supervised with paired data and/or prohibitively expensive fully-sampled MRI sequences. Further, reconstruction networks typically rely on convolutional architectures which are limited in their capacity to model long-range interactions and may lead to suboptimal recovery of fine anatomical detail. To these ends, we present a dual-domain self-supervised transformer (DSFormer) for accelerated MC-MRI reconstruction. DSFormer develops a deep conditional cascade transformer (DCCT) consisting of several cascaded Swin transformer reconstruction networks (SwinRN) trained under two deep conditioning strategies to enable MC-MRI information sharing. We further present a dual-domain (image and k-space) self-supervised learning strategy for DCCT to alleviate the costs of acquiring fully sampled training data. DSFormer generates high-fidelity reconstructions which experimentally outperform current fully-supervised baselines. Moreover, we find that DSFormer achieves nearly the same performance when trained either with full supervision or with our proposed dual-domain self-supervision.