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arXiv2023

Consistency-guided Meta-Learning for Bootstrapping Semi-Supervised Medical Image Segmentation

Medical imaging has witnessed remarkable progress but usually requires a large amount of high-quality annotated data which is time-consuming and costly to obtain. To alleviate this burden, semi-supervised learning has garnered attention as a potential solution. In this paper, we present Meta-Learning for Bootstrapping Medical Image Segmentation (MLB-Seg), a novel method for tackling the challenge of semi-supervised medical image segmentation. Specifically, our approach first involves training a segmentation model on a small set of clean labeled images to generate initial labels for unlabeled data. To further optimize this bootstrapping process, we introduce a per-pixel weight mapping system that dynamically assigns weights to both the initialized labels and the model's own predictions. These weights are determined using a meta-process that prioritizes pixels with loss gradient directions closer to those of clean data, which is based on a small set of precisely annotated images. To facilitate the meta-learning process, we additionally introduce a consistency-based Pseudo Label Enhancement (PLE) scheme that improves the quality of the model's own predictions by ensembling predictions from various augmented versions of the same input. In order to improve the quality of the weight maps obtained through multiple augmentations of a single input, we introduce a mean teacher into the PLE scheme. This method helps to reduce noise in the weight maps and stabilize its generation process. Our extensive experimental results on public atrial and prostate segmentation datasets demonstrate that our proposed method achieves state-of-the-art results under semi-supervision. Our code is available at https://github.com/aijinrjinr/MLB-Seg.

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arXiv2024

HiDiff: Hybrid Diffusion Framework for Medical Image Segmentation

Medical image segmentation has been significantly advanced with the rapid development of deep learning (DL) techniques. Existing DL-based segmentation models are typically discriminative; i.e., they aim to learn a mapping from the input image to segmentation masks. However, these discriminative methods neglect the underlying data distribution and intrinsic class characteristics, suffering from unstable feature space. In this work, we propose to complement discriminative segmentation methods with the knowledge of underlying data distribution from generative models. To that end, we propose a novel hybrid diffusion framework for medical image segmentation, termed HiDiff, which can synergize the strengths of existing discriminative segmentation models and new generative diffusion models. HiDiff comprises two key components: discriminative segmentor and diffusion refiner. First, we utilize any conventional trained segmentation models as discriminative segmentor, which can provide a segmentation mask prior for diffusion refiner. Second, we propose a novel binary Bernoulli diffusion model (BBDM) as the diffusion refiner, which can effectively, efficiently, and interactively refine the segmentation mask by modeling the underlying data distribution. Third, we train the segmentor and BBDM in an alternate-collaborative manner to mutually boost each other. Extensive experimental results on abdomen organ, brain tumor, polyps, and retinal vessels segmentation datasets, covering four widely-used modalities, demonstrate the superior performance of HiDiff over existing medical segmentation algorithms, including the state-of-the-art transformer- and diffusion-based ones. In addition, HiDiff excels at segmenting small objects and generalizing to new datasets. Source codes are made available at https://github.com/takimailto/HiDiff.

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arXiv2026

UltraSAM3: A Concept-Driven Foundation Model for Universal Ultrasound Image Segmentation

Ultrasound imaging has become increasingly widespread in clinical practice due to its portability, low cost and real-time capability, making ultrasound image segmentation important. However, ultrasound images differ substantially from CT, MRI, and other medical imaging modalities, as they are often affected by speckle noise, low contrast, acoustic shadows and ambiguous boundaries. Existing ultrasound segmentation methods are still mainly limited to task-specific models or visual-prompt-based foundation models, which are either tailored to particular tasks or require expert-provided visual prompts, making them inconvenient for flexible clinical use. To address these challenges, we propose UltraSAM3, a concept-driven foundation model for universal ultrasound image segmentation. Unlike conventional models, UltraSAM3 enables text-based target specification by adapting SAM3 to ultrasound-specific image--mask--concept triplets. The model is trained on a large-scale ultrasound segmentation corpus covering 37 public datasets and 13 anatomical categories, allowing it to align ultrasound visual patterns with clinically meaningful concepts across diverse organs and lesions. To further improve usability under realistic clinical interaction, we propose an instruction-guided agent that parses complex natural language queries into concise ultrasound concept prompts for UltraSAM3. Extensive experiments demonstrate that UltraSAM3 consistently outperforms representative concept- and text-driven biomedical segmentation models on multi-organ ultrasound benchmarks, external datasets, and visual-prompt-enhanced settings. Moreover, the agent improves segmentation robustness for complex user instructions. These results indicate that ultrasound-specific concept adaptation is effective for building generalizable and interactive ultrasound segmentation foundation models.

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arXiv2022

A Study on the Use of Edge TPUs for Eye Fundus Image Segmentation

Medical image segmentation can be implemented using Deep Learning methods with fast and efficient segmentation networks. Single-board computers (SBCs) are difficult to use to train deep networks due to their memory and processing limitations. Specific hardware such as Google's Edge TPU makes them suitable for real time predictions using complex pre-trained networks. In this work, we study the performance of two SBCs, with and without hardware acceleration for fundus image segmentation, though the conclusions of this study can be applied to the segmentation by deep neural networks of other types of medical images. To test the benefits of hardware acceleration, we use networks and datasets from a previous published work and generalize them by testing with a dataset with ultrasound thyroid images. We measure prediction times in both SBCs and compare them with a cloud based TPU system. The results show the feasibility of Machine Learning accelerated SBCs for optic disc and cup segmentation obtaining times below 25 milliseconds per image using Edge TPUs.

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arXiv2023

Focused and Collaborative Feedback Integration for Interactive Image Segmentation

Interactive image segmentation aims at obtaining a segmentation mask for an image using simple user annotations. During each round of interaction, the segmentation result from the previous round serves as feedback to guide the user's annotation and provides dense prior information for the segmentation model, effectively acting as a bridge between interactions. Existing methods overlook the importance of feedback or simply concatenate it with the original input, leading to underutilization of feedback and an increase in the number of required annotations. To address this, we propose an approach called Focused and Collaborative Feedback Integration (FCFI) to fully exploit the feedback for click-based interactive image segmentation. FCFI first focuses on a local area around the new click and corrects the feedback based on the similarities of high-level features. It then alternately and collaboratively updates the feedback and deep features to integrate the feedback into the features. The efficacy and efficiency of FCFI were validated on four benchmarks, namely GrabCut, Berkeley, SBD, and DAVIS. Experimental results show that FCFI achieved new state-of-the-art performance with less computational overhead than previous methods. The source code is available at https://github.com/veizgyauzgyauz/FCFI.

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arXiv2024

MSA$^2$Net: Multi-scale Adaptive Attention-guided Network for Medical Image Segmentation

Medical image segmentation involves identifying and separating object instances in a medical image to delineate various tissues and structures, a task complicated by the significant variations in size, shape, and density of these features. Convolutional neural networks (CNNs) have traditionally been used for this task but have limitations in capturing long-range dependencies. Transformers, equipped with self-attention mechanisms, aim to address this problem. However, in medical image segmentation it is beneficial to merge both local and global features to effectively integrate feature maps across various scales, capturing both detailed features and broader semantic elements for dealing with variations in structures. In this paper, we introduce MSA$^2$Net, a new deep segmentation framework featuring an expedient design of skip-connections. These connections facilitate feature fusion by dynamically weighting and combining coarse-grained encoder features with fine-grained decoder feature maps. Specifically, we propose a Multi-Scale Adaptive Spatial Attention Gate (MASAG), which dynamically adjusts the receptive field (Local and Global contextual information) to ensure that spatially relevant features are selectively highlighted while minimizing background distractions. Extensive evaluations involving dermatology, and radiological datasets demonstrate that our MSA$^2$Net outperforms state-of-the-art (SOTA) works or matches their performance. The source code is publicly available at https://github.com/xmindflow/MSA-2Net.

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arXiv2023

MMNet: Multi-Mask Network for Referring Image Segmentation

Referring image segmentation aims to segment an object referred to by natural language expression from an image. However, this task is challenging due to the distinct data properties between text and image, and the randomness introduced by diverse objects and unrestricted language expression. Most of previous work focus on improving cross-modal feature fusion while not fully addressing the inherent uncertainty caused by diverse objects and unrestricted language. To tackle these problems, we propose an end-to-end Multi-Mask Network for referring image segmentation(MMNet). we first combine picture and language and then employ an attention mechanism to generate multiple queries that represent different aspects of the language expression. We then utilize these queries to produce a series of corresponding segmentation masks, assigning a score to each mask that reflects its importance. The final result is obtained through the weighted sum of all masks, which greatly reduces the randomness of the language expression. Our proposed framework demonstrates superior performance compared to state-of-the-art approaches on the two most commonly used datasets, RefCOCO, RefCOCO+ and G-Ref, without the need for any post-processing. This further validates the efficacy of our proposed framework.

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arXiv2023

Boundary Difference Over Union Loss For Medical Image Segmentation

Medical image segmentation is crucial for clinical diagnosis. However, current losses for medical image segmentation mainly focus on overall segmentation results, with fewer losses proposed to guide boundary segmentation. Those that do exist often need to be used in combination with other losses and produce ineffective results. To address this issue, we have developed a simple and effective loss called the Boundary Difference over Union Loss (Boundary DoU Loss) to guide boundary region segmentation. It is obtained by calculating the ratio of the difference set of prediction and ground truth to the union of the difference set and the partial intersection set. Our loss only relies on region calculation, making it easy to implement and training stable without needing any additional losses. Additionally, we use the target size to adaptively adjust attention applied to the boundary regions. Experimental results using UNet, TransUNet, and Swin-UNet on two datasets (ACDC and Synapse) demonstrate the effectiveness of our proposed loss function. Code is available at https://github.com/sunfan-bvb/BoundaryDoULoss.

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arXiv2021

Semantic-Aware Contrastive Learning for Multi-object Medical Image Segmentation

Medical image segmentation, or computing voxelwise semantic masks, is a fundamental yet challenging task to compute a voxel-level semantic mask. To increase the ability of encoder-decoder neural networks to perform this task across large clinical cohorts, contrastive learning provides an opportunity to stabilize model initialization and enhance encoders without labels. However, multiple target objects (with different semantic meanings) may exist in a single image, which poses a problem for adapting traditional contrastive learning methods from prevalent 'image-level classification' to 'pixel-level segmentation'. In this paper, we propose a simple semantic-aware contrastive learning approach leveraging attention masks to advance multi-object semantic segmentation. Briefly, we embed different semantic objects to different clusters rather than the traditional image-level embeddings. We evaluate our proposed method on a multi-organ medical image segmentation task with both in-house data and MICCAI Challenge 2015 BTCV datasets. Compared with current state-of-the-art training strategies, our proposed pipeline yields a substantial improvement of 5.53% and 6.09% on Dice score for both medical image segmentation cohorts respectively (p-value<0.01). The performance of the proposed method is further assessed on natural images via the PASCAL VOC 2012 dataset, and achieves a substantial improvement of 2.75% on mIoU (p-value<0.01).

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arXiv2026

Test-time generative augmentation for medical image segmentation

Medical image segmentation is critical for clinical diagnosis, treatment planning, and monitoring, yet segmentation models often struggle with uncertainties stemming from occlusions, ambiguous boundaries, and variations in imaging devices. Traditional test-time augmentation (TTA) techniques typically rely on predefined geometric and photometric transformations, limiting their adaptability and effectiveness in complex medical scenarios. In this study, we introduced Test-Time Generative Augmentation (TTGA), a novel augmentation strategy specifically tailored for medical image segmentation at inference time. Different from conventional augmentation strategies that suffer from excessive randomness or limited flexibility, TTGA leverages a domain-fine-tuned generative model to produce contextually relevant and diverse augmentations tailored to the characteristics of each test image. Built upon diffusion model inversion, a masked null-text inversion method is proposed to enable region-specific augmentations during sampling. Furthermore, a dual denoising pathway is designed to balance precise identity preservation with controlled variability. We demonstrate the efficacy of our TTGA through extensive experiments across three distinct segmentation tasks spanning nine datasets. Our results consistently demonstrate that TTGA not only improves segmentation accuracy (with DSC gains ranging from 0.1% to 2.3% over the baseline) but also offers pixel-wise error estimation (with DSC gains ranging from 1.1% to 29.0% over the baseline). The source code and demonstration are available at: https://github.com/maxiao0234/TTGA.

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arXiv2021

A Large-Scale Benchmark for Food Image Segmentation

Food image segmentation is a critical and indispensible task for developing health-related applications such as estimating food calories and nutrients. Existing food image segmentation models are underperforming due to two reasons: (1) there is a lack of high quality food image datasets with fine-grained ingredient labels and pixel-wise location masks -- the existing datasets either carry coarse ingredient labels or are small in size; and (2) the complex appearance of food makes it difficult to localize and recognize ingredients in food images, e.g., the ingredients may overlap one another in the same image, and the identical ingredient may appear distinctly in different food images. In this work, we build a new food image dataset FoodSeg103 (and its extension FoodSeg154) containing 9,490 images. We annotate these images with 154 ingredient classes and each image has an average of 6 ingredient labels and pixel-wise masks. In addition, we propose a multi-modality pre-training approach called ReLeM that explicitly equips a segmentation model with rich and semantic food knowledge. In experiments, we use three popular semantic segmentation methods (i.e., Dilated Convolution based, Feature Pyramid based, and Vision Transformer based) as baselines, and evaluate them as well as ReLeM on our new datasets. We believe that the FoodSeg103 (and its extension FoodSeg154) and the pre-trained models using ReLeM can serve as a benchmark to facilitate future works on fine-grained food image understanding. We make all these datasets and methods public at \url{https://xiongweiwu.github.io/foodseg103.html}.

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arXiv2023

HybridMIM: A Hybrid Masked Image Modeling Framework for 3D Medical Image Segmentation

Masked image modeling (MIM) with transformer backbones has recently been exploited as a powerful self-supervised pre-training technique. The existing MIM methods adopt the strategy to mask random patches of the image and reconstruct the missing pixels, which only considers semantic information at a lower level, and causes a long pre-training time.This paper presents HybridMIM, a novel hybrid self-supervised learning method based on masked image modeling for 3D medical image segmentation.Specifically, we design a two-level masking hierarchy to specify which and how patches in sub-volumes are masked, effectively providing the constraints of higher level semantic information. Then we learn the semantic information of medical images at three levels, including:1) partial region prediction to reconstruct key contents of the 3D image, which largely reduces the pre-training time burden (pixel-level); 2) patch-masking perception to learn the spatial relationship between the patches in each sub-volume (region-level).and 3) drop-out-based contrastive learning between samples within a mini-batch, which further improves the generalization ability of the framework (sample-level). The proposed framework is versatile to support both CNN and transformer as encoder backbones, and also enables to pre-train decoders for image segmentation. We conduct comprehensive experiments on four widely-used public medical image segmentation datasets, including BraTS2020, BTCV, MSD Liver, and MSD Spleen. The experimental results show the clear superiority of HybridMIM against competing supervised methods, masked pre-training approaches, and other self-supervised methods, in terms of quantitative metrics, timing performance and qualitative observations. The codes of HybridMIM are available at https://github.com/ge-xing/HybridMIM

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arXiv2025

UNet with Self-Adaptive Mamba-Like Attention and Causal-Resonance Learning for Medical Image Segmentation

Medical image segmentation plays an important role in various clinical applications; however, existing deep learning models face trade-offs between efficiency and accuracy. Convolutional Neural Networks (CNNs) capture local details well but miss the global context, whereas transformers handle the global context but at a high computational cost. Recently, State Space Sequence Models (SSMs) have shown potential for capturing long-range dependencies with linear complexity; however, their direct use in medical image segmentation remains limited due to incompatibility with image structures and autoregressive assumptions. To overcome these challenges, we propose SAMA-UNet, a novel U-shaped architecture that introduces two key innovations. First, the Self-Adaptive Mamba-like Aggregated Attention (SAMA) block adaptively integrates local and global features through dynamic attention weighting, enabling an efficient representation of complex anatomical patterns. Second, the causal resonance multi-scale module (CR-MSM) improves encoder-decoder interactions by adjusting feature resolution and causal dependencies across scales, enhancing the semantic alignment between low- and high-level features. Extensive experiments on MRI, CT, and endoscopy datasets demonstrate that SAMA-UNet consistently outperforms CNN, Transformer, and Mamba-based methods. It achieves 85.38% DSC and 87.82% NSD on BTCV, 92.16% and 96.54% on ACDC, 67.14% and 68.70% on EndoVis17, and 84.06% and 88.47% on ATLAS23, establishing new benchmarks across modalities. These results confirm the effectiveness of SAMA-UNet in combining efficiency and accuracy, making it a promising solution for real-world clinical segmentation tasks. The source code is available on GitHub.

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arXiv2010

A Robust Fuzzy Clustering Technique with Spatial Neighborhood Information for Effective Medical Image Segmentation

Medical image segmentation demands an efficient and robust segmentation algorithm against noise. The conventional fuzzy c-means algorithm is an efficient clustering algorithm that is used in medical image segmentation. But FCM is highly vulnerable to noise since it uses only intensity values for clustering the images. This paper aims to develop a novel and efficient fuzzy spatial c-means clustering algorithm which is robust to noise. The proposed clustering algorithm uses fuzzy spatial information to calculate membership value. The input image is clustered using proposed ISFCM algorithm. A comparative study has been made between the conventional FCM and proposed ISFCM. The proposed approach is found to be outperforming the conventional FCM.

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arXiv2025

Hi-End-MAE: Hierarchical encoder-driven masked autoencoders are stronger vision learners for medical image segmentation

Medical image segmentation remains a formidable challenge due to the label scarcity. Pre-training Vision Transformer (ViT) through masked image modeling (MIM) on large-scale unlabeled medical datasets presents a promising solution, providing both computational efficiency and model generalization for various downstream tasks. However, current ViT-based MIM pre-training frameworks predominantly emphasize local aggregation representations in output layers and fail to exploit the rich representations across different ViT layers that better capture fine-grained semantic information needed for more precise medical downstream tasks. To fill the above gap, we hereby present Hierarchical Encoder-driven MAE (Hi-End-MAE), a simple yet effective ViT-based pre-training solution, which centers on two key innovations: (1) Encoder-driven reconstruction, which encourages the encoder to learn more informative features to guide the reconstruction of masked patches; and (2) Hierarchical dense decoding, which implements a hierarchical decoding structure to capture rich representations across different layers. We pre-train Hi-End-MAE on a large-scale dataset of 10K CT scans and evaluated its performance across seven public medical image segmentation benchmarks. Extensive experiments demonstrate that Hi-End-MAE achieves superior transfer learning capabilities across various downstream tasks, revealing the potential of ViT in medical imaging applications. The code is available at: https://github.com/FengheTan9/Hi-End-MAE

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arXiv2025

MambaVesselNet++: A Hybrid CNN-Mamba Architecture for Medical Image Segmentation

Medical image segmentation plays an important role in computer-aided diagnosis. Traditional convolution-based U-shape segmentation architectures are usually limited by the local receptive field. Existing vision transformers have been widely applied to diverse medical segmentation frameworks due to their superior capabilities of capturing global contexts. Despite the advantage, the real-world application of vision transformers is challenged by their non-linear self-attention mechanism, requiring huge computational costs. To address this issue, the selective state space model (SSM) Mamba has gained recognition for its adeptness in modeling long-range dependencies in sequential data, particularly noted for its efficient memory costs. In this paper, we propose MambaVesselNet++, a Hybrid CNN-Mamba framework for medical image segmentation. Our MambaVesselNet++ is comprised of a hybrid image encoder (Hi-Encoder) and a bifocal fusion decoder (BF-Decoder). In Hi-Encoder, we first devise the texture-aware layer to capture low-level semantic features by leveraging convolutions. Then, we utilize Mamba to effectively model long-range dependencies with linear complexity. The Bi-Decoder adopts skip connections to combine local and global information of the Hi-Encoder for the accurate generation of segmentation masks. Extensive experiments demonstrate that MambaVesselNet++ outperforms current convolution-based, transformer-based, and Mamba-based state-of-the-arts across diverse medical 2D, 3D, and instance segmentation tasks. The code is available at https://github.com/CC0117/MambaVesselNet.

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arXiv2022

CRIS: CLIP-Driven Referring Image Segmentation

Referring image segmentation aims to segment a referent via a natural linguistic expression.Due to the distinct data properties between text and image, it is challenging for a network to well align text and pixel-level features. Existing approaches use pretrained models to facilitate learning, yet separately transfer the language/vision knowledge from pretrained models, ignoring the multi-modal corresponding information. Inspired by the recent advance in Contrastive Language-Image Pretraining (CLIP), in this paper, we propose an end-to-end CLIP-Driven Referring Image Segmentation framework (CRIS). To transfer the multi-modal knowledge effectively, CRIS resorts to vision-language decoding and contrastive learning for achieving the text-to-pixel alignment. More specifically, we design a vision-language decoder to propagate fine-grained semantic information from textual representations to each pixel-level activation, which promotes consistency between the two modalities. In addition, we present text-to-pixel contrastive learning to explicitly enforce the text feature similar to the related pixel-level features and dissimilar to the irrelevances. The experimental results on three benchmark datasets demonstrate that our proposed framework significantly outperforms the state-of-the-art performance without any post-processing. The code will be released.

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arXiv2023

Semantics-Aware Dynamic Localization and Refinement for Referring Image Segmentation

Referring image segmentation segments an image from a language expression. With the aim of producing high-quality masks, existing methods often adopt iterative learning approaches that rely on RNNs or stacked attention layers to refine vision-language features. Despite their complexity, RNN-based methods are subject to specific encoder choices, while attention-based methods offer limited gains. In this work, we introduce a simple yet effective alternative for progressively learning discriminative multi-modal features. The core idea of our approach is to leverage a continuously updated query as the representation of the target object and at each iteration, strengthen multi-modal features strongly correlated to the query while weakening less related ones. As the query is initialized by language features and successively updated by object features, our algorithm gradually shifts from being localization-centric to segmentation-centric. This strategy enables the incremental recovery of missing object parts and/or removal of extraneous parts through iteration. Compared to its counterparts, our method is more versatile$\unicode{x2014}$it can be plugged into prior arts straightforwardly and consistently bring improvements. Experimental results on the challenging datasets of RefCOCO, RefCOCO+, and G-Ref demonstrate its advantage with respect to the state-of-the-art methods.

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