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arXiv2023

Curriculum-Based Augmented Fourier Domain Adaptation for Robust Medical Image Segmentation

Accurate and robust medical image segmentation is fundamental and crucial for enhancing the autonomy of computer-aided diagnosis and intervention systems. Medical data collection normally involves different scanners, protocols, and populations, making domain adaptation (DA) a highly demanding research field to alleviate model degradation in the deployment site. To preserve the model performance across multiple testing domains, this work proposes the Curriculum-based Augmented Fourier Domain Adaptation (Curri-AFDA) for robust medical image segmentation. In particular, our curriculum learning strategy is based on the causal relationship of a model under different levels of data shift in the deployment phase, where the higher the shift is, the harder to recognize the variance. Considering this, we progressively introduce more amplitude information from the target domain to the source domain in the frequency space during the curriculum-style training to smoothly schedule the semantic knowledge transfer in an easier-to-harder manner. Besides, we incorporate the training-time chained augmentation mixing to help expand the data distributions while preserving the domain-invariant semantics, which is beneficial for the acquired model to be more robust and generalize better to unseen domains. Extensive experiments on two segmentation tasks of Retina and Nuclei collected from multiple sites and scanners suggest that our proposed method yields superior adaptation and generalization performance. Meanwhile, our approach proves to be more robust under various corruption types and increasing severity levels. In addition, we show our method is also beneficial in the domain-adaptive classification task with skin lesion datasets. The code is available at https://github.com/lofrienger/Curri-AFDA.

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arXiv2021

Deep Class-Specific Affinity-Guided Convolutional Network for Multimodal Unpaired Image Segmentation

Multi-modal medical image segmentation plays an essential role in clinical diagnosis. It remains challenging as the input modalities are often not well-aligned spatially. Existing learning-based methods mainly consider sharing trainable layers across modalities and minimizing visual feature discrepancies. While the problem is often formulated as joint supervised feature learning, multiple-scale features and class-specific representation have not yet been explored. In this paper, we propose an affinity-guided fully convolutional network for multimodal image segmentation. To learn effective representations, we design class-specific affinity matrices to encode the knowledge of hierarchical feature reasoning, together with the shared convolutional layers to ensure the cross-modality generalization. Our affinity matrix does not depend on spatial alignments of the visual features and thus allows us to train with unpaired, multimodal inputs. We extensively evaluated our method on two public multimodal benchmark datasets and outperform state-of-the-art methods.

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arXiv2022

Personalizing Federated Medical Image Segmentation via Local Calibration

Medical image segmentation under federated learning (FL) is a promising direction by allowing multiple clinical sites to collaboratively learn a global model without centralizing datasets. However, using a single model to adapt to various data distributions from different sites is extremely challenging. Personalized FL tackles this issue by only utilizing partial model parameters shared from global server, while keeping the rest to adapt to its own data distribution in the local training of each site. However, most existing methods concentrate on the partial parameter splitting, while do not consider the \textit{inter-site in-consistencies} during the local training, which in fact can facilitate the knowledge communication over sites to benefit the model learning for improving the local accuracy. In this paper, we propose a personalized federated framework with \textbf{L}ocal \textbf{C}alibration (LC-Fed), to leverage the inter-site in-consistencies in both \textit{feature- and prediction- levels} to boost the segmentation. Concretely, as each local site has its alternative attention on the various features, we first design the contrastive site embedding coupled with channel selection operation to calibrate the encoded features. Moreover, we propose to exploit the knowledge of prediction-level in-consistency to guide the personalized modeling on the ambiguous regions, e.g., anatomical boundaries. It is achieved by computing a disagreement-aware map to calibrate the prediction. Effectiveness of our method has been verified on three medical image segmentation tasks with different modalities, where our method consistently shows superior performance to the state-of-the-art personalized FL methods. Code is available at https://github.com/jcwang123/FedLC.

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arXiv2024

LKM-UNet: Large Kernel Vision Mamba UNet for Medical Image Segmentation

In clinical practice, medical image segmentation provides useful information on the contours and dimensions of target organs or tissues, facilitating improved diagnosis, analysis, and treatment. In the past few years, convolutional neural networks (CNNs) and Transformers have dominated this area, but they still suffer from either limited receptive fields or costly long-range modeling. Mamba, a State Space Sequence Model (SSM), recently emerged as a promising paradigm for long-range dependency modeling with linear complexity. In this paper, we introduce a Large Kernel Vision Mamba U-shape Network, or LKM-UNet, for medical image segmentation. A distinguishing feature of our LKM-UNet is its utilization of large Mamba kernels, excelling in locally spatial modeling compared to small kernel-based CNNs and Transformers, while maintaining superior efficiency in global modeling compared to self-attention with quadratic complexity. Additionally, we design a novel hierarchical and bidirectional Mamba block to further enhance Mamba's global and neighborhood spatial modeling capability for vision inputs. Comprehensive experiments demonstrate the feasibility and the effectiveness of using large-size Mamba kernels to achieve large receptive fields. Codes are available at https://github.com/wjh892521292/LKM-UNet.

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arXiv2025

MLRU++: Multiscale Lightweight Residual UNETR++ with Attention for Efficient 3D Medical Image Segmentation

Accurate and efficient medical image segmentation is crucial but challenging due to anatomical variability and high computational demands on volumetric data. Recent hybrid CNN-Transformer architectures achieve state-of-the-art results but add significant complexity. In this paper, we propose MLRU++, a Multiscale Lightweight Residual UNETR++ architecture designed to balance segmentation accuracy and computational efficiency. It introduces two key innovations: a Lightweight Channel and Bottleneck Attention Module (LCBAM) that enhances contextual feature encoding with minimal overhead, and a Multiscale Bottleneck Block (M2B) in the decoder that captures fine-grained details via multi-resolution feature aggregation. Experiments on four publicly available benchmark datasets (Synapse, BTCV, ACDC, and Decathlon Lung) demonstrate that MLRU++ achieves state-of-the-art performance, with average Dice scores of 87.57% (Synapse), 93.00% (ACDC), and 81.12% (Lung). Compared to existing leading models, MLRU++ improves Dice scores by 5.38% and 2.12% on Synapse and ACDC, respectively, while significantly reducing parameter count and computational cost. Ablation studies evaluating LCBAM and M2B further confirm the effectiveness of the proposed architectural components. Results suggest that MLRU++ offers a practical and high-performing solution for 3D medical image segmentation tasks. Source code is available at: https://github.com/1027865/MLRUPP

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arXiv2023

ScribbleVC: Scribble-supervised Medical Image Segmentation with Vision-Class Embedding

Medical image segmentation plays a critical role in clinical decision-making, treatment planning, and disease monitoring. However, accurate segmentation of medical images is challenging due to several factors, such as the lack of high-quality annotation, imaging noise, and anatomical differences across patients. In addition, there is still a considerable gap in performance between the existing label-efficient methods and fully-supervised methods. To address the above challenges, we propose ScribbleVC, a novel framework for scribble-supervised medical image segmentation that leverages vision and class embeddings via the multimodal information enhancement mechanism. In addition, ScribbleVC uniformly utilizes the CNN features and Transformer features to achieve better visual feature extraction. The proposed method combines a scribble-based approach with a segmentation network and a class-embedding module to produce accurate segmentation masks. We evaluate ScribbleVC on three benchmark datasets and compare it with state-of-the-art methods. The experimental results demonstrate that our method outperforms existing approaches in terms of accuracy, robustness, and efficiency. The datasets and code are released on GitHub.

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arXiv2025

Dual-Alignment Knowledge Retention for Continual Medical Image Segmentation

Continual learning in medical image segmentation involves sequential data acquisition across diverse domains (e.g., clinical sites), where task interference between past and current domains often leads to catastrophic forgetting. Existing continual learning methods fail to capture the complex dependencies between tasks. We introduce a novel framework that mitigates forgetting by establishing and enhancing complex dependencies between historical data and the network in the present task. Our framework features a dual-alignment strategy, the cross-network alignment (CNA) module aligns the features extracted from the bottleneck layers of the current and previous networks, respectively, while the cross-representation alignment (CRA) module aligns the features learned by the current network from historical buffered data and current input data, respectively. Implementing both types of alignment is a non-trivial task. To address this, we further analyze the linear and nonlinear forms of the well-established Hilbert-Schmidt Independence Criterion (HSIC) and deliberately design feature mapping and feature pairing blocks within the CRA module. Experiments on medical image segmentation task demonstrate our framework's effectiveness in mitigating catastrophic forgetting under domain shifts.

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arXiv2026

BBR-Net: Boundary-Balanced Replay for Continual Medical Image Segmentation

Continual learning for medical image segmentation remains challenging under domain shift because replay-based methods often preserve appearance information without explicitly modeling anatomical structure. This study investigates whether structural consistency governs knowledge retention in continual cardiac ultrasound segmentation. We propose the Boundary-Balanced Replay Network (BBR-Net), which selects replay samples using boundary-aware priority and class balance to preserve anatomically informative regions. The method is evaluated on CAMUS and CardiacNet under forward (CAMUS to CardiacNet) and reverse (CardiacNet to CAMUS) task orders. In the forward setting, BBR-Net retains source-task performance close to an offline joint-training reference, while markedly reducing catastrophic forgetting and preserving competitive target-task adaptation. Ablation results show that boundary-aware prioritization contributes to retention and improves the balance between source-task preservation and target-task adaptation when combined with class-aware sampling. In contrast, the reverse setting reveals that structure-aware replay fails when initial representations are learned from noisy and structurally inconsistent data. To isolate this effect, we conduct a controlled structural perturbation analysis by progressively corrupting source-task boundaries while keeping the dataset, architecture, and training protocol fixed. Forgetting increases consistently as structural reliability decreases, suggesting that replay effectiveness is strongly influenced by the quality of stored structural information, rather than by memory capacity alone. These findings indicate that preserving anatomical structure under domain shift is a central factor in continual medical image segmentation, and that replay mechanisms should account for structural reliability to support robust knowledge retention.

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arXiv2016

Bacterial foraging optimization based brain magnetic resonance image segmentation

Segmentation partitions an image into its constituent parts. It is essentially the pre-processing stage of image analysis and computer vision. In this work, T1 and T2 weighted brain magnetic resonance images are segmented using multilevel thresholding and bacterial foraging optimization (BFO) algorithm. The thresholds are obtained by maximizing the between class variance (multilevel Otsu method) of the image. The BFO algorithm is used to optimize the threshold searching process. The edges are then obtained from the thresholded image by comparing the intensity of each pixel with its eight connected neighbourhood. Post processing is performed to remove spurious responses in the segmented image. The proposed segmentation technique is evaluated using edge detector evaluation parameters such as figure of merit, Rand Index and variation of information. The proposed brain MR image segmentation technique outperforms the traditional edge detectors such as canny and sobel.

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arXiv2026

Accuracy Improvement of Cell Image Segmentation Using Feedback Former

Semantic segmentation of microscopy cell images by deep learning is a significant technique. We considered that the Transformers, which have recently outperformed CNNs in image recognition, could also be improved and developed for cell image segmentation. Transformers tend to focus more on contextual information than on detailed information. This tendency leads to a lack of detailed information for segmentation. Therefore, to supplement or reinforce the missing detailed information, we hypothesized that feedback processing in the human visual cortex should be effective. Our proposed Feedback Former is a novel architecture for semantic segmentation, in which Transformers is used as an encoder and has a feedback processing mechanism. Feature maps with detailed information are fed back to the lower layers from near the output of the model to compensate for the lack of detailed information which is the weakness of Transformers and improve the segmentation accuracy. By experiments on three cell image datasets, we confirmed that our method surpasses methods without feedback, demonstrating its superior accuracy in cell image segmentation. Our method achieved higher segmentation accuracy while consuming less computational cost than conventional feedback approaches. Moreover, our method offered superior precision without simply increasing the model size of Transformer encoder, demonstrating higher accuracy with lower computational cost.

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arXiv2025

Static Segmentation by Tracking: A Label-Efficient Approach for Fine-Grained Specimen Image Segmentation

We study image segmentation in the biological domain, particularly trait segmentation from specimen images (e.g., butterfly wing stripes, beetle elytra). This fine-grained task is crucial for understanding the biology of organisms, but it traditionally requires manually annotating segmentation masks for hundreds of images per species, making it highly labor-intensive. To address this challenge, we propose a label-efficient approach, Static Segmentation by Tracking (SST), based on a key insight: while specimens of the same species exhibit natural variation, the traits of interest show up consistently. This motivates us to concatenate specimen images into a ``pseudo-video'' and reframe trait segmentation as a tracking problem. Specifically, SST generates masks for unlabeled images by propagating annotated or predicted masks from the ``pseudo-preceding'' images. Built upon recent video segmentation models, such as Segment Anything Model 2, SST achieves high-quality trait segmentation with only one labeled image per species, marking a breakthrough in specimen image analysis. To further enhance segmentation quality, we introduce a cycle-consistent loss for fine-tuning, again requiring only one labeled image. Additionally, we demonstrate the broader potential of SST, including one-shot instance segmentation in natural images and trait-based image retrieval.

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arXiv2024

Beyond Adapting SAM: Towards End-to-End Ultrasound Image Segmentation via Auto Prompting

End-to-end medical image segmentation is of great value for computer-aided diagnosis dominated by task-specific models, usually suffering from poor generalization. With recent breakthroughs brought by the segment anything model (SAM) for universal image segmentation, extensive efforts have been made to adapt SAM for medical imaging but still encounter two major issues: 1) severe performance degradation and limited generalization without proper adaptation, and 2) semi-automatic segmentation relying on accurate manual prompts for interaction. In this work, we propose SAMUS as a universal model tailored for ultrasound image segmentation and further enable it to work in an end-to-end manner denoted as AutoSAMUS. Specifically, in SAMUS, a parallel CNN branch is introduced to supplement local information through cross-branch attention, and a feature adapter and a position adapter are jointly used to adapt SAM from natural to ultrasound domains while reducing training complexity. AutoSAMUS is realized by introducing an auto prompt generator (APG) to replace the manual prompt encoder of SAMUS to automatically generate prompt embeddings. A comprehensive ultrasound dataset, comprising about 30k images and 69k masks and covering six object categories, is collected for verification. Extensive comparison experiments demonstrate the superiority of SAMUS and AutoSAMUS against the state-of-the-art task-specific and SAM-based foundation models. We believe the auto-prompted SAM-based model has the potential to become a new paradigm for end-to-end medical image segmentation and deserves more exploration. Code and data are available at https://github.com/xianlin7/SAMUS.

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arXiv2024

A Bottom-Up Approach to Class-Agnostic Image Segmentation

Class-agnostic image segmentation is a crucial component in automating image editing workflows, especially in contexts where object selection traditionally involves interactive tools. Existing methods in the literature often adhere to top-down formulations, following the paradigm of class-based approaches, where object detection precedes per-object segmentation. In this work, we present a novel bottom-up formulation for addressing the class-agnostic segmentation problem. We supervise our network directly on the projective sphere of its feature space, employing losses inspired by metric learning literature as well as losses defined in a novel segmentation-space representation. The segmentation results are obtained through a straightforward mean-shift clustering of the estimated features. Our bottom-up formulation exhibits exceptional generalization capability, even when trained on datasets designed for class-based segmentation. We further showcase the effectiveness of our generic approach by addressing the challenging task of cell and nucleus segmentation. We believe that our bottom-up formulation will offer valuable insights into diverse segmentation challenges in the literature.

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arXiv2024

Multi-rater Prompting for Ambiguous Medical Image Segmentation

Multi-rater annotations commonly occur when medical images are independently annotated by multiple experts (raters). In this paper, we tackle two challenges arisen in multi-rater annotations for medical image segmentation (called ambiguous medical image segmentation): (1) How to train a deep learning model when a group of raters produces a set of diverse but plausible annotations, and (2) how to fine-tune the model efficiently when computation resources are not available for re-training the entire model on a different dataset domain. We propose a multi-rater prompt-based approach to address these two challenges altogether. Specifically, we introduce a series of rater-aware prompts that can be plugged into the U-Net model for uncertainty estimation to handle multi-annotation cases. During the prompt-based fine-tuning process, only 0.3% of learnable parameters are required to be updated comparing to training the entire model. Further, in order to integrate expert consensus and disagreement, we explore different multi-rater incorporation strategies and design a mix-training strategy for comprehensive insight learning. Extensive experiments verify the effectiveness of our new approach for ambiguous medical image segmentation on two public datasets while alleviating the heavy burden of model re-training.

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arXiv2021

Finding an Unsupervised Image Segmenter in Each of Your Deep Generative Models

Recent research has shown that numerous human-interpretable directions exist in the latent space of GANs. In this paper, we develop an automatic procedure for finding directions that lead to foreground-background image separation, and we use these directions to train an image segmentation model without human supervision. Our method is generator-agnostic, producing strong segmentation results with a wide range of different GAN architectures. Furthermore, by leveraging GANs pretrained on large datasets such as ImageNet, we are able to segment images from a range of domains without further training or finetuning. Evaluating our method on image segmentation benchmarks, we compare favorably to prior work while using neither human supervision nor access to the training data. Broadly, our results demonstrate that automatically extracting foreground-background structure from pretrained deep generative models can serve as a remarkably effective substitute for human supervision.

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arXiv2020

Dual Convolutional LSTM Network for Referring Image Segmentation

We consider referring image segmentation. It is a problem at the intersection of computer vision and natural language understanding. Given an input image and a referring expression in the form of a natural language sentence, the goal is to segment the object of interest in the image referred by the linguistic query. To this end, we propose a dual convolutional LSTM (ConvLSTM) network to tackle this problem. Our model consists of an encoder network and a decoder network, where ConvLSTM is used in both encoder and decoder networks to capture spatial and sequential information. The encoder network extracts visual and linguistic features for each word in the expression sentence, and adopts an attention mechanism to focus on words that are more informative in the multimodal interaction. The decoder network integrates the features generated by the encoder network at multiple levels as its input and produces the final precise segmentation mask. Experimental results on four challenging datasets demonstrate that the proposed network achieves superior segmentation performance compared with other state-of-the-art methods.

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arXiv2025

UKBOB: One Billion MRI Labeled Masks for Generalizable 3D Medical Image Segmentation

In medical imaging, the primary challenge is collecting large-scale labeled data due to privacy concerns, logistics, and high labeling costs. In this work, we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset of body organs, comprising 51,761 MRI 3D samples (equivalent to 17.9 million 2D images) and more than 1.37 billion 2D segmentation masks of 72 organs, all based on the UK Biobank MRI dataset. We utilize automatic labeling, introduce an automated label cleaning pipeline with organ-specific filters, and manually annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality (referred to as UKBOB-manual). This approach allows for scaling up the dataset collection while maintaining confidence in the labels. We further confirm the validity of the labels by demonstrating zero-shot generalization of trained models on the filtered UKBOB to other small labeled datasets from similar domains (e.g., abdominal MRI). To further mitigate the effect of noisy labels, we propose a novel method called Entropy Test-time Adaptation (ETTA) to refine the segmentation output. We use UKBOB to train a foundation model, Swin-BOB, for 3D medical image segmentation based on the Swin-UNetr architecture, achieving state-of-the-art results in several benchmarks in 3D medical imaging, including the BRATS brain MRI tumor challenge (with a 0.4% improvement) and the BTCV abdominal CT scan benchmark (with a 1.3% improvement). The pre-trained models and the code are available at https://emmanuelleb985.github.io/ukbob , and the filtered labels will be made available with the UK Biobank.

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arXiv2024

SAM2-Adapter: Evaluating & Adapting Segment Anything 2 in Downstream Tasks: Camouflage, Shadow, Medical Image Segmentation, and More

The advent of large models, also known as foundation models, has significantly transformed the AI research landscape, with models like Segment Anything (SAM) achieving notable success in diverse image segmentation scenarios. Despite its advancements, SAM encountered limitations in handling some complex low-level segmentation tasks like camouflaged object and medical imaging. In response, in 2023, we introduced SAM-Adapter, which demonstrated improved performance on these challenging tasks. Now, with the release of Segment Anything 2 (SAM2), a successor with enhanced architecture and a larger training corpus, we reassess these challenges. This paper introduces SAM2-Adapter, the first adapter designed to overcome the persistent limitations observed in SAM2 and achieve new state-of-the-art (SOTA) results in specific downstream tasks including medical image segmentation, camouflaged (concealed) object detection, and shadow detection. SAM2-Adapter builds on the SAM-Adapter's strengths, offering enhanced generalizability and composability for diverse applications. We present extensive experimental results demonstrating SAM2-Adapter's effectiveness. We show the potential and encourage the research community to leverage the SAM2 model with our SAM2-Adapter for achieving superior segmentation outcomes. Code, pre-trained models, and data processing protocols are available at http://tianrun-chen.github.io/SAM-Adaptor/

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