Cycle-Consistent Bridge Diffusion Model for Accelerated MRI Reconstruction

Accelerated MRI reconstruction techniques aim to reduce examination time while maintaining high image fidelity, which is highly desirable in clinical settings for improving patient comfort and hospital efficiency. Existing deep learning methods typically reconstruct images from under-sampled data with traditional reconstruction approaches, but they still struggle to provide high-fidelity results. Diffusion models show great potential to improve fidelity of generated images in recent years. However, their inference process starting with a random Gaussian noise introduces instability into the results and usually requires thousands of sampling steps, resulting in sub-optimal reconstruction quality and low efficiency. To address these challenges, we propose Cycle-Consistent Bridge Diffusion Model (CBDM). CBDM employs two bridge diffusion models to construct a cycle-consistent diffusion process with a consistency loss, enhancing the fine-grained details of reconstructed images and reducing the number of diffusion steps. Moreover, CBDM incorporates a Contourlet Decomposition Embedding Module (CDEM) which captures multi-scale structural texture knowledge in images through frequency domain decomposition pyramids and directional filter banks to improve structural fidelity. Extensive experiments demonstrate the superiority of our model by higher reconstruction quality and fewer training iterations, achieving a new state of the art for accelerated MRI reconstruction in both fastMRI and IXI datasets.

Cross Group Attention and Group-wise Rolling for Multimodal Medical Image Synthesis

Multimodal MR image synthesis aims to generate missing modality image by fusing and mapping a few available MRI data. Most existing approaches typically adopt an image-to-image translation scheme. However, these methods often suffer from sub-optimal performance due to the spatial misalignment between different modalities while they are typically treated as input channels. Therefore, in this paper, we propose an Adaptive Group-wise Interaction Network (AGI-Net) that explores both inter-modality and intra-modality relationships for multimodal MR image synthesis. Specifically, groups are first pre-defined along the channel dimension and then we perform an adaptive rolling for the standard convolutional kernel to capture inter-modality spatial correspondences. At the same time, a cross-group attention module is introduced to fuse information across different channel groups, leading to better feature representation. We evaluated the effectiveness of our model on the publicly available IXI and BraTS2023 datasets, where the AGI-Net achieved state-of-the-art performance for multimodal MR image synthesis. Code will be released.

Weakly Supervised Lymph Nodes Segmentation Based on Partial Instance Annotations with Pre-trained Dual-branch Network and Pseudo Label Learning

Assessing the presence of potentially malignant lymph nodes aids in estimating cancer progression, and identifying surrounding benign lymph nodes can assist in determining potential metastatic pathways for cancer. For quantitative analysis, automatic segmentation of lymph nodes is crucial. However, due to the labor-intensive and time-consuming manual annotation process required for a large number of lymph nodes, it is more practical to annotate only a subset of the lymph node instances to reduce annotation costs. In this study, we propose a pre-trained Dual-Branch network with Dynamically Mixed Pseudo label (DBDMP) to learn from partial instance annotations for lymph nodes segmentation. To obtain reliable pseudo labels for lymph nodes that are not annotated, we employ a dual-decoder network to generate different outputs that are then dynamically mixed. We integrate the original weak partial annotations with the mixed pseudo labels to supervise the network. To further leverage the extensive amount of unannotated voxels, we apply a self-supervised pre-training strategy to enhance the model's feature extraction capability. Experiments on the mediastinal Lymph Node Quantification (LNQ) dataset demonstrate that our method, compared to directly learning from partial instance annotations, significantly improves the Dice Similarity Coefficient (DSC) from 11.04% to 54.10% and reduces the Average Symmetric Surface Distance (ASSD) from 20.83 $mm$ to 8.72 $mm$. The code is available at https://github.com/WltyBY/LNQ2023_training_code.git

SAM-Driven Weakly Supervised Nodule Segmentation with Uncertainty-Aware Cross Teaching

Automated nodule segmentation is essential for computer-assisted diagnosis in ultrasound images. Nevertheless, most existing methods depend on precise pixel-level annotations by medical professionals, a process that is both costly and labor-intensive. Recently, segmentation foundation models like SAM have shown impressive generalizability on natural images, suggesting their potential as pseudo-labelers. However, accurate prompts remain crucial for their success in medical images. In this work, we devise a novel weakly supervised framework that effectively utilizes the segmentation foundation model to generate pseudo-labels from aspect ration annotations for automatic nodule segmentation. Specifically, we develop three types of bounding box prompts based on scalable shape priors, followed by an adaptive pseudo-label selection module to fully exploit the prediction capabilities of the foundation model for nodules. We also present a SAM-driven uncertainty-aware cross-teaching strategy. This approach integrates SAM-based uncertainty estimation and label-space perturbations into cross-teaching to mitigate the impact of pseudo-label inaccuracies on model training. Extensive experiments on two clinically collected ultrasound datasets demonstrate the superior performance of our proposed method.

An Uncertainty-guided Tiered Self-training Framework for Active Source-free Domain Adaptation in Prostate Segmentation

Deep learning models have exhibited remarkable efficacy in accurately delineating the prostate for diagnosis and treatment of prostate diseases, but challenges persist in achieving robust generalization across different medical centers. Source-free Domain Adaptation (SFDA) is a promising technique to adapt deep segmentation models to address privacy and security concerns while reducing domain shifts between source and target domains. However, recent literature indicates that the performance of SFDA remains far from satisfactory due to unpredictable domain gaps. Annotating a few target domain samples is acceptable, as it can lead to significant performance improvement with a low annotation cost. Nevertheless, due to extremely limited annotation budgets, careful consideration is needed in selecting samples for annotation. Inspired by this, our goal is to develop Active Source-free Domain Adaptation (ASFDA) for medical image segmentation. Specifically, we propose a novel Uncertainty-guided Tiered Self-training (UGTST) framework, consisting of efficient active sample selection via entropy-based primary local peak filtering to aggregate global uncertainty and diversity-aware redundancy filter, coupled with a tiered self-learning strategy, achieves stable domain adaptation. Experimental results on cross-center prostate MRI segmentation datasets revealed that our method yielded marked advancements, with a mere 5% annotation, exhibiting an average Dice score enhancement of 9.78% and 7.58% in two target domains compared with state-of-the-art methods, on par with fully supervised learning. Code is available at:https://github.com/HiLab-git/UGTST

Advancing UWF-SLO Vessel Segmentation with Source-Free Active Domain Adaptation and a Novel Multi-Center Dataset

Accurate vessel segmentation in Ultra-Wide-Field Scanning Laser Ophthalmoscopy (UWF-SLO) images is crucial for diagnosing retinal diseases. Although recent techniques have shown encouraging outcomes in vessel segmentation, models trained on one medical dataset often underperform on others due to domain shifts. Meanwhile, manually labeling high-resolution UWF-SLO images is an extremely challenging, time-consuming and expensive task. In response, this study introduces a pioneering framework that leverages a patch-based active domain adaptation approach. By actively recommending a few valuable image patches by the devised Cascade Uncertainty-Predominance (CUP) selection strategy for labeling and model-finetuning, our method significantly improves the accuracy of UWF-SLO vessel segmentation across diverse medical centers. In addition, we annotate and construct the first Multi-center UWF-SLO Vessel Segmentation (MU-VS) dataset to promote this topic research, comprising data from multiple institutions. This dataset serves as a valuable resource for cross-center evaluation, verifying the effectiveness and robustness of our approach. Experimental results demonstrate that our approach surpasses existing domain adaptation and active learning methods, considerably reducing the gap between the Upper and Lower bounds with minimal annotations, highlighting our method's practical clinical value. We will release our dataset and code to facilitate relevant research: https://github.com/whq-xxh/SFADA-UWF-SLO.

Rethinking Abdominal Organ Segmentation (RAOS) in the clinical scenario: A robustness evaluation benchmark with challenging cases

Deep learning has enabled great strides in abdominal multi-organ segmentation, even surpassing junior oncologists on common cases or organs. However, robustness on corner cases and complex organs remains a challenging open problem for clinical adoption. To investigate model robustness, we collected and annotated the RAOS dataset comprising 413 CT scans ($\sim$80k 2D images, $\sim$8k 3D organ annotations) from 413 patients each with 17 (female) or 19 (male) labelled organs, manually delineated by oncologists. We grouped scans based on clinical information into 1) diagnosis/radiotherapy (317 volumes), 2) partial excision without the whole organ missing (22 volumes), and 3) excision with the whole organ missing (74 volumes). RAOS provides a potential benchmark for evaluating model robustness including organ hallucination. It also includes some organs that can be very hard to access on public datasets like the rectum, colon, intestine, prostate and seminal vesicles. We benchmarked several state-of-the-art methods in these three clinical groups to evaluate performance and robustness. We also assessed cross-generalization between RAOS and three public datasets. This dataset and comprehensive analysis establish a potential baseline for future robustness research: \url{https://github.com/Luoxd1996/RAOS}.

Ultrasound Nodule Segmentation Using Asymmetric Learning with Simple Clinical Annotation

Recent advances in deep learning have greatly facilitated the automated segmentation of ultrasound images, which is essential for nodule morphological analysis. Nevertheless, most existing methods depend on extensive and precise annotations by domain experts, which are labor-intensive and time-consuming. In this study, we suggest using simple aspect ratio annotations directly from ultrasound clinical diagnoses for automated nodule segmentation. Especially, an asymmetric learning framework is developed by extending the aspect ratio annotations with two types of pseudo labels, i.e., conservative labels and radical labels, to train two asymmetric segmentation networks simultaneously. Subsequently, a conservative-radical-balance strategy (CRBS) strategy is proposed to complementally combine radical and conservative labels. An inconsistency-aware dynamically mixed pseudo-labels supervision (IDMPS) module is introduced to address the challenges of over-segmentation and under-segmentation caused by the two types of labels. To further leverage the spatial prior knowledge provided by clinical annotations, we also present a novel loss function namely the clinical anatomy prior loss. Extensive experiments on two clinically collected ultrasound datasets (thyroid and breast) demonstrate the superior performance of our proposed method, which can achieve comparable and even better performance than fully supervised methods using ground truth annotations.

Diversified and Personalized Multi-rater Medical Image Segmentation

Annotation ambiguity due to inherent data uncertainties such as blurred boundaries in medical scans and different observer expertise and preferences has become a major obstacle for training deep-learning based medical image segmentation models. To address it, the common practice is to gather multiple annotations from different experts, leading to the setting of multi-rater medical image segmentation. Existing works aim to either merge different annotations into the "groundtruth" that is often unattainable in numerous medical contexts, or generate diverse results, or produce personalized results corresponding to individual expert raters. Here, we bring up a more ambitious goal for multi-rater medical image segmentation, i.e., obtaining both diversified and personalized results. Specifically, we propose a two-stage framework named D-Persona (first Diversification and then Personalization). In Stage I, we exploit multiple given annotations to train a Probabilistic U-Net model, with a bound-constrained loss to improve the prediction diversity. In this way, a common latent space is constructed in Stage I, where different latent codes denote diversified expert opinions. Then, in Stage II, we design multiple attention-based projection heads to adaptively query the corresponding expert prompts from the shared latent space, and then perform the personalized medical image segmentation. We evaluated the proposed model on our in-house Nasopharyngeal Carcinoma dataset and the public lung nodule dataset (i.e., LIDC-IDRI). Extensive experiments demonstrated our D-Persona can provide diversified and personalized results at the same time, achieving new SOTA performance for multi-rater medical image segmentation. Our code will be released at https://github.com/ycwu1997/D-Persona.

SegRap2023: A Benchmark of Organs-at-Risk and Gross Tumor Volume Segmentation for Radiotherapy Planning of Nasopharyngeal Carcinoma

Radiation therapy is a primary and effective NasoPharyngeal Carcinoma (NPC) treatment strategy. The precise delineation of Gross Tumor Volumes (GTVs) and Organs-At-Risk (OARs) is crucial in radiation treatment, directly impacting patient prognosis. Previously, the delineation of GTVs and OARs was performed by experienced radiation oncologists. Recently, deep learning has achieved promising results in many medical image segmentation tasks. However, for NPC OARs and GTVs segmentation, few public datasets are available for model development and evaluation. To alleviate this problem, the SegRap2023 challenge was organized in conjunction with MICCAI2023 and presented a large-scale benchmark for OAR and GTV segmentation with 400 Computed Tomography (CT) scans from 200 NPC patients, each with a pair of pre-aligned non-contrast and contrast-enhanced CT scans. The challenge's goal was to segment 45 OARs and 2 GTVs from the paired CT scans. In this paper, we detail the challenge and analyze the solutions of all participants. The average Dice similarity coefficient scores for all submissions ranged from 76.68\% to 86.70\%, and 70.42\% to 73.44\% for OARs and GTVs, respectively. We conclude that the segmentation of large-size OARs is well-addressed, and more efforts are needed for GTVs and small-size or thin-structure OARs. The benchmark will remain publicly available here: https://segrap2023.grand-challenge.org