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Transformers have revolutionized medical image restoration, but the quadratic complexity still poses limitations for their application to high-resolution medical images. The recent advent of RWKV in the NLP field has attracted much attention as it can process long sequences efficiently. To leverage its advanced design, we propose Restore-RWKV, the first RWKV-based model for medical image restoration. Since the original RWKV model is designed for 1D sequences, we make two necessary modifications for modeling spatial relations in 2D images. First, we present a recurrent WKV (Re-WKV) attention mechanism that captures global dependencies with linear computational complexity. Re-WKV incorporates bidirectional attention as basic for a global receptive field and recurrent attention to effectively model 2D dependencies from various scan directions. Second, we develop an omnidirectional token shift (Omni-Shift) layer that enhances local dependencies by shifting tokens from all directions and across a wide context range. These adaptations make the proposed Restore-RWKV an efficient and effective model for medical image restoration. Extensive experiments demonstrate that Restore-RWKV achieves superior performance across various medical image restoration tasks, including MRI image super-resolution, CT image denoising, PET image synthesis, and all-in-one medical image restoration. Code is available at: \href{https://github.com/Yaziwel/Restore-RWKV.git}{https://github.com/Yaziwel/Restore-RWKV}., Comment: This paper introduces the first RWKV-based model for image restoration

Transformer-based methods have demonstrated impressive results in medical image restoration, attributed to the multi-head self-attention (MSA) mechanism in the spatial dimension. However, the majority of existing Transformers conduct attention within fixed and coarsely partitioned regions (\text{e.g.} the entire image or fixed patches), resulting in interference from irrelevant regions and fragmentation of continuous image content. To overcome these challenges, we introduce a novel Region Attention Transformer (RAT) that utilizes a region-based multi-head self-attention mechanism (R-MSA). The R-MSA dynamically partitions the input image into non-overlapping semantic regions using the robust Segment Anything Model (SAM) and then performs self-attention within these regions. This region partitioning is more flexible and interpretable, ensuring that only pixels from similar semantic regions complement each other, thereby eliminating interference from irrelevant regions. Moreover, we introduce a focal region loss to guide our model to adaptively focus on recovering high-difficulty regions. Extensive experiments demonstrate the effectiveness of RAT in various medical image restoration tasks, including PET image synthesis, CT image denoising, and pathological image super-resolution. Code is available at \href{https://github.com/Yaziwel/Region-Attention-Transformer-for-Medical-Image-Restoration.git}{https://github.com/RAT}., Comment: This paper has been accepted by MICCAI 2024

Although single-task medical image restoration (MedIR) has witnessed remarkable success, the limited generalizability of these methods poses a substantial obstacle to wider application. In this paper, we focus on the task of all-in-one medical image restoration, aiming to address multiple distinct MedIR tasks with a single universal model. Nonetheless, due to significant differences between different MedIR tasks, training a universal model often encounters task interference issues, where different tasks with shared parameters may conflict with each other in the gradient update direction. This task interference leads to deviation of the model update direction from the optimal path, thereby affecting the model's performance. To tackle this issue, we propose a task-adaptive routing strategy, allowing conflicting tasks to select different network paths in spatial and channel dimensions, thereby mitigating task interference. Experimental results demonstrate that our proposed \textbf{A}ll-in-one \textbf{M}edical \textbf{I}mage \textbf{R}estoration (\textbf{AMIR}) network achieves state-of-the-art performance in three MedIR tasks: MRI super-resolution, CT denoising, and PET synthesis, both in single-task and all-in-one settings. The code and data will be available at \href{https://github.com/Yaziwel/All-In-One-Medical-Image-Restoration-via-Task-Adaptive-Routing.git}{https://github.com/Yaziwel/AMIR}., Comment: This article has been early accepted by MICCAI 2024

Image-guided depth completion aims at generating a dense depth map from sparse LiDAR data and RGB image. Recent methods have shown promising performance by reformulating it as a classification problem with two sub-tasks: depth discretization and probability prediction. They divide the depth range into several discrete depth values as depth categories, serving as priors for scene depth distributions. However, previous depth discretization methods are easy to be impacted by depth distribution variations across different scenes, resulting in suboptimal scene depth distribution priors. To address the above problem, we propose a progressive depth decoupling and modulating network, which incrementally decouples the depth range into bins and adaptively generates multi-scale dense depth maps in multiple stages. Specifically, we first design a Bins Initializing Module (BIM) to construct the seed bins by exploring the depth distribution information within a sparse depth map, adapting variations of depth distribution. Then, we devise an incremental depth decoupling branch to progressively refine the depth distribution information from global to local. Meanwhile, an adaptive depth modulating branch is developed to progressively improve the probability representation from coarse-grained to fine-grained. And the bi-directional information interactions are proposed to strengthen the information interaction between those two branches (sub-tasks) for promoting information complementation in each branch. Further, we introduce a multi-scale supervision mechanism to learn the depth distribution information in latent features and enhance the adaptation capability across different scenes. Experimental results on public datasets demonstrate that our method outperforms the state-of-the-art methods. The code will be open-sourced at [this https URL](https://github.com/Cisse-away/PDDM)., Comment: The article is accepted by IEEE Transactions on Instrumentation & Measurement

Multi-center positron emission tomography (PET) image synthesis aims at recovering low-dose PET images from multiple different centers. The generalizability of existing methods can still be suboptimal for a multi-center study due to domain shifts, which result from non-identical data distribution among centers with different imaging systems/protocols. While some approaches address domain shifts by training specialized models for each center, they are parameter inefficient and do not well exploit the shared knowledge across centers. To address this, we develop a generalist model that shares architecture and parameters across centers to utilize the shared knowledge. However, the generalist model can suffer from the center interference issue, \textit{i.e.} the gradient directions of different centers can be inconsistent or even opposite owing to the non-identical data distribution. To mitigate such interference, we introduce a novel dynamic routing strategy with cross-layer connections that routes data from different centers to different experts. Experiments show that our generalist model with dynamic routing (DRMC) exhibits excellent generalizability across centers. Code and data are available at: https://github.com/Yaziwel/Multi-Center-PET-Image-Synthesis., Comment: This article has been early accepted by MICCAI 2023,but has not been fully edited. Content may change prior to final publication

Potential radioactive hazards in full-dose positron emission tomography (PET) imaging remain a concern, whereas the quality of low-dose images is never desirable for clinical use. So it is of great interest to translate low-dose PET images into full-dose. Previous studies based on deep learning methods usually directly extract hierarchical features for reconstruction. We notice that the importance of each feature is different and they should be weighted dissimilarly so that tiny information can be captured by the neural network. Furthermore, the synthesis on some regions of interest is important in some applications. Here we propose a novel segmentation guided style-based generative adversarial network (SGSGAN) for PET synthesis. (1) We put forward a style-based generator employing style modulation, which specifically controls the hierarchical features in the translation process, to generate images with more realistic textures. (2) We adopt a task-driven strategy that couples a segmentation task with a generative adversarial network (GAN) framework to improve the translation performance. Extensive experiments show the superiority of our overall framework in PET synthesis, especially on those regions of interest., Comment: This article has been accepted for publication in a future issue of this journal, but has not been fully edited. Content may change prior to final publication. Citation information: DOI 10.1109/TMI.2022.3156614, IEEE Transactions on Medical Imaging

It is difficult to accurately label ambiguous and complex shaped targets manually by binary masks. The weakness of binary mask under-expression is highlighted in medical image segmentation, where blurring is prevalent. In the case of multiple annotations, reaching a consensus for clinicians by binary masks is more challenging. Moreover, these uncertain areas are related to the lesions' structure and may contain anatomical information beneficial to diagnosis. However, current studies on uncertainty mainly focus on the uncertainty in model training and data labels. None of them investigate the influence of the ambiguous nature of the lesion itself.Inspired by image matting, this paper introduces alpha matte as a soft mask to represent uncertain areas in medical scenes and accordingly puts forward a new uncertainty quantification method to fill the gap of uncertainty research for lesion structure. In this work, we introduce a new architecture to generate binary masks and alpha mattes in a multitasking framework, which outperforms all state-of-the-art matting algorithms compared. The proposed uncertainty map is able to highlight the ambiguous regions and a novel multitasking loss weighting strategy we presented can improve performance further and demonstrate their concrete benefits. To fully-evaluate the effectiveness of our proposed method, we first labelled three medical datasets with alpha matte to address the shortage of available matting datasets in medical scenes and prove the alpha matte to be a more efficient labeling method than a binary mask from both qualitative and quantitative aspects., Comment: Jounal version of our MICCAI 2021 paper, in review