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arXiv2024

SelfReg-UNet: Self-Regularized UNet for Medical Image Segmentation

Since its introduction, UNet has been leading a variety of medical image segmentation tasks. Although numerous follow-up studies have also been dedicated to improving the performance of standard UNet, few have conducted in-depth analyses of the underlying interest pattern of UNet in medical image segmentation. In this paper, we explore the patterns learned in a UNet and observe two important factors that potentially affect its performance: (i) irrelative feature learned caused by asymmetric supervision; (ii) feature redundancy in the feature map. To this end, we propose to balance the supervision between encoder and decoder and reduce the redundant information in the UNet. Specifically, we use the feature map that contains the most semantic information (i.e., the last layer of the decoder) to provide additional supervision to other blocks to provide additional supervision and reduce feature redundancy by leveraging feature distillation. The proposed method can be easily integrated into existing UNet architecture in a plug-and-play fashion with negligible computational cost. The experimental results suggest that the proposed method consistently improves the performance of standard UNets on four medical image segmentation datasets. The code is available at \url{https://github.com/ChongQingNoSubway/SelfReg-UNet}

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arXiv2024

Modality-agnostic Domain Generalizable Medical Image Segmentation by Multi-Frequency in Multi-Scale Attention

Generalizability in deep neural networks plays a pivotal role in medical image segmentation. However, deep learning-based medical image analyses tend to overlook the importance of frequency variance, which is critical element for achieving a model that is both modality-agnostic and domain-generalizable. Additionally, various models fail to account for the potential information loss that can arise from multi-task learning under deep supervision, a factor that can impair the model representation ability. To address these challenges, we propose a Modality-agnostic Domain Generalizable Network (MADGNet) for medical image segmentation, which comprises two key components: a Multi-Frequency in Multi-Scale Attention (MFMSA) block and Ensemble Sub-Decoding Module (E-SDM). The MFMSA block refines the process of spatial feature extraction, particularly in capturing boundary features, by incorporating multi-frequency and multi-scale features, thereby offering informative cues for tissue outline and anatomical structures. Moreover, we propose E-SDM to mitigate information loss in multi-task learning with deep supervision, especially during substantial upsampling from low resolution. We evaluate the segmentation performance of MADGNet across six modalities and fifteen datasets. Through extensive experiments, we demonstrate that MADGNet consistently outperforms state-of-the-art models across various modalities, showcasing superior segmentation performance. This affirms MADGNet as a robust solution for medical image segmentation that excels in diverse imaging scenarios. Our MADGNet code is available in GitHub Link.

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arXiv2022

Cross-level Contrastive Learning and Consistency Constraint for Semi-supervised Medical Image Segmentation

Semi-supervised learning (SSL), which aims at leveraging a few labeled images and a large number of unlabeled images for network training, is beneficial for relieving the burden of data annotation in medical image segmentation. According to the experience of medical imaging experts, local attributes such as texture, luster and smoothness are very important factors for identifying target objects like lesions and polyps in medical images. Motivated by this, we propose a cross-level contrastive learning scheme to enhance representation capacity for local features in semi-supervised medical image segmentation. Compared to existing image-wise, patch-wise and point-wise contrastive learning algorithms, our devised method is capable of exploring more complex similarity cues, namely the relational characteristics between global and local patch-wise representations. Additionally, for fully making use of cross-level semantic relations, we devise a novel consistency constraint that compares the predictions of patches against those of the full image. With the help of the cross-level contrastive learning and consistency constraint, the unlabelled data can be effectively explored to improve segmentation performance on two medical image datasets for polyp and skin lesion segmentation respectively. Code of our approach is available.

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arXiv2023

Grouping Boundary Proposals for Fast Interactive Image Segmentation

Geodesic models are known as an efficient tool for solving various image segmentation problems. Most of existing approaches only exploit local pointwise image features to track geodesic paths for delineating the objective boundaries. However, such a segmentation strategy cannot take into account the connectivity of the image edge features, increasing the risk of shortcut problem, especially in the case of complicated scenario. In this work, we introduce a new image segmentation model based on the minimal geodesic framework in conjunction with an adaptive cut-based circular optimal path computation scheme and a graph-based boundary proposals grouping scheme. Specifically, the adaptive cut can disconnect the image domain such that the target contours are imposed to pass through this cut only once. The boundary proposals are comprised of precomputed image edge segments, providing the connectivity information for our segmentation model. These boundary proposals are then incorporated into the proposed image segmentation model, such that the target segmentation contours are made up of a set of selected boundary proposals and the corresponding geodesic paths linking them. Experimental results show that the proposed model indeed outperforms state-of-the-art minimal paths-based image segmentation approaches.

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arXiv2024

Exploring Fine-Grained Image-Text Alignment for Referring Remote Sensing Image Segmentation

Given a language expression, referring remote sensing image segmentation (RRSIS) aims to identify ground objects and assign pixel-wise labels within the imagery. The one of key challenges for this task is to capture discriminative multi-modal features via text-image alignment. However, the existing RRSIS methods use one vanilla and coarse alignment, where the language expression is directly extracted to be fused with the visual features. In this paper, we argue that a ``fine-grained image-text alignment'' can improve the extraction of multi-modal information. To this point, we propose a new referring remote sensing image segmentation method to fully exploit the visual and linguistic representations. Specifically, the original referring expression is regarded as context text, which is further decoupled into the ground object and spatial position texts. The proposed fine-grained image-text alignment module (FIAM) would simultaneously leverage the features of the input image and the corresponding texts, obtaining better discriminative multi-modal representation. Meanwhile, to handle the various scales of ground objects in remote sensing, we introduce a Text-aware Multi-scale Enhancement Module (TMEM) to adaptively perform cross-scale fusion and intersections. We evaluate the effectiveness of the proposed method on two public referring remote sensing datasets including RefSegRS and RRSIS-D, and our method obtains superior performance over several state-of-the-art methods. The code will be publicly available at https://github.com/Shaosifan/FIANet.

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arXiv2026

Med-2D SegNet: A Light Weight Deep Neural Network for Medical 2D Image Segmentation

Accurate and efficient medical image segmentation is crucial for advancing clinical diagnostics and surgical planning, yet remains a complex challenge due to the variability in anatomical structures and the demand for low-complexity models. In this paper, we introduced Med-2D SegNet, a novel and highly efficient segmentation architecture that delivers outstanding accuracy while maintaining a minimal computational footprint. Med-2D SegNet achieves state-of-the-art performance across multiple benchmark datasets, including KVASIR-SEG, PH2, EndoVis, and GLAS, with an average Dice similarity coefficient (DSC) of 89.77% across 20 diverse datasets. Central to its success is the compact Med Block, a specialized encoder design that incorporates dimension expansion and parameter reduction, enabling precise feature extraction while keeping model parameters to a low count of just 2.07 million. Med-2D SegNet excels in cross-dataset generalization, particularly in polyp segmentation, where it was trained on KVASIR-SEG and showed strong performance on unseen datasets, demonstrating its robustness in zero-shot learning scenarios, even though we acknowledge that further improvements are possible. With top-tier performance in both binary and multi-class segmentation, Med-2D SegNet redefines the balance between accuracy and efficiency, setting a new benchmark for medical image analysis. This work paves the way for developing accessible, high-performance diagnostic tools suitable for clinical environments and resource-constrained settings, making it a step forward in the democratization of advanced medical technology.

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arXiv2024

A Simple Image Segmentation Framework via In-Context Examples

Recently, there have been explorations of generalist segmentation models that can effectively tackle a variety of image segmentation tasks within a unified in-context learning framework. However, these methods still struggle with task ambiguity in in-context segmentation, as not all in-context examples can accurately convey the task information. In order to address this issue, we present SINE, a simple image Segmentation framework utilizing in-context examples. Our approach leverages a Transformer encoder-decoder structure, where the encoder provides high-quality image representations, and the decoder is designed to yield multiple task-specific output masks to effectively eliminate task ambiguity. Specifically, we introduce an In-context Interaction module to complement in-context information and produce correlations between the target image and the in-context example and a Matching Transformer that uses fixed matching and a Hungarian algorithm to eliminate differences between different tasks. In addition, we have further perfected the current evaluation system for in-context image segmentation, aiming to facilitate a holistic appraisal of these models. Experiments on various segmentation tasks show the effectiveness of the proposed method.

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arXiv2017

Importance of Image Enhancement Techniques in Color Image Segmentation: A Comprehensive and Comparative Study

Color image segmentation is a very emerging research topic in the area of color image analysis and pattern recognition. Many state-of-the-art algorithms have been developed for this purpose. But, often the segmentation results of these algorithms seem to be suffering from miss-classifications and over-segmentation. The reasons behind these are the degradation of image quality during the acquisition, transmission and color space conversion. So, here arises the need of an efficient image enhancement technique which can remove the redundant pixels or noises from the color image before proceeding for final segmentation. In this paper, an effort has been made to study and analyze different image enhancement techniques and thereby finding out the better one for color image segmentation. Also, this comparative study is done on two well-known color spaces HSV and LAB separately to find out which color space supports segmentation task more efficiently with respect to those enhancement techniques.

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arXiv2024

Beyond Pixel-Wise Supervision for Medical Image Segmentation: From Traditional Models to Foundation Models

Medical image segmentation plays an important role in many image-guided clinical approaches. However, existing segmentation algorithms mostly rely on the availability of fully annotated images with pixel-wise annotations for training, which can be both labor-intensive and expertise-demanding, especially in the medical imaging domain where only experts can provide reliable and accurate annotations. To alleviate this challenge, there has been a growing focus on developing segmentation methods that can train deep models with weak annotations, such as image-level, bounding boxes, scribbles, and points. The emergence of vision foundation models, notably the Segment Anything Model (SAM), has introduced innovative capabilities for segmentation tasks using weak annotations for promptable segmentation enabled by large-scale pre-training. Adopting foundation models together with traditional learning methods has increasingly gained recent interest research community and shown potential for real-world applications. In this paper, we present a comprehensive survey of recent progress on annotation-efficient learning for medical image segmentation utilizing weak annotations before and in the era of foundation models. Furthermore, we analyze and discuss several challenges of existing approaches, which we believe will provide valuable guidance for shaping the trajectory of foundational models to further advance the field of medical image segmentation.

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arXiv2024

MSVM-UNet: Multi-Scale Vision Mamba UNet for Medical Image Segmentation

State Space Models (SSMs), especially Mamba, have shown great promise in medical image segmentation due to their ability to model long-range dependencies with linear computational complexity. However, accurate medical image segmentation requires the effective learning of both multi-scale detailed feature representations and global contextual dependencies. Although existing works have attempted to address this issue by integrating CNNs and SSMs to leverage their respective strengths, they have not designed specialized modules to effectively capture multi-scale feature representations, nor have they adequately addressed the directional sensitivity problem when applying Mamba to 2D image data. To overcome these limitations, we propose a Multi-Scale Vision Mamba UNet model for medical image segmentation, termed MSVM-UNet. Specifically, by introducing multi-scale convolutions in the VSS blocks, we can more effectively capture and aggregate multi-scale feature representations from the hierarchical features of the VMamba encoder and better handle 2D visual data. Additionally, the large kernel patch expanding (LKPE) layers achieve more efficient upsampling of feature maps by simultaneously integrating spatial and channel information. Extensive experiments on the Synapse and ACDC datasets demonstrate that our approach is more effective than some state-of-the-art methods in capturing and aggregating multi-scale feature representations and modeling long-range dependencies between pixels.

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arXiv2018

BoxNet: Deep Learning Based Biomedical Image Segmentation Using Boxes Only Annotation

In recent years, deep learning (DL) methods have become powerful tools for biomedical image segmentation. However, high annotation efforts and costs are commonly needed to acquire sufficient biomedical training data for DL models. To alleviate the burden of manual annotation, in this paper, we propose a new weakly supervised DL approach for biomedical image segmentation using boxes only annotation. First, we develop a method to combine graph search (GS) and DL to generate fine object masks from box annotation, in which DL uses box annotation to compute a rough segmentation for GS and then GS is applied to locate the optimal object boundaries. During the mask generation process, we carefully utilize information from box annotation to filter out potential errors, and then use the generated masks to train an accurate DL segmentation network. Extensive experiments on gland segmentation in histology images, lymph node segmentation in ultrasound images, and fungus segmentation in electron microscopy images show that our approach attains superior performance over the best known state-of-the-art weakly supervised DL method and is able to achieve (1) nearly the same accuracy compared to fully supervised DL methods with far less annotation effort, (2) significantly better results with similar annotation time, and (3) robust performance in various applications.

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arXiv2023

Multi-Level Global Context Cross Consistency Model for Semi-Supervised Ultrasound Image Segmentation with Diffusion Model

Medical image segmentation is a critical step in computer-aided diagnosis, and convolutional neural networks are popular segmentation networks nowadays. However, the inherent local operation characteristics make it difficult to focus on the global contextual information of lesions with different positions, shapes, and sizes. Semi-supervised learning can be used to learn from both labeled and unlabeled samples, alleviating the burden of manual labeling. However, obtaining a large number of unlabeled images in medical scenarios remains challenging. To address these issues, we propose a Multi-level Global Context Cross-consistency (MGCC) framework that uses images generated by a Latent Diffusion Model (LDM) as unlabeled images for semi-supervised learning. The framework involves of two stages. In the first stage, a LDM is used to generate synthetic medical images, which reduces the workload of data annotation and addresses privacy concerns associated with collecting medical data. In the second stage, varying levels of global context noise perturbation are added to the input of the auxiliary decoder, and output consistency is maintained between decoders to improve the representation ability. Experiments conducted on open-source breast ultrasound and private thyroid ultrasound datasets demonstrate the effectiveness of our framework in bridging the probability distribution and the semantic representation of the medical image. Our approach enables the effective transfer of probability distribution knowledge to the segmentation network, resulting in improved segmentation accuracy. The code is available at https://github.com/FengheTan9/Multi-Level-Global-Context-Cross-Consistency.

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arXiv2024

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.

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arXiv2025

Dual-Scale Volume Priors with Wasserstein-Based Consistency for Semi-Supervised Medical Image Segmentation

Despite signi cant progress in semi-supervised medical image segmentation, most existing segmentation networks overlook e ective methodological guidance for feature extraction and important prior information from datasets. In this paper, we develop a semi-supervised medical image segmentation framework that e ectively integrates spatial regularization methods and volume priors. Speci cally, our approach integrates a strong explicit volume prior at the image scale and Threshold Dynamics spatial regularization, both derived from variational models, into the backbone segmentation network. The target region volumes for each unlabeled image are estimated by a regression network, which e ectively regularizes the backbone segmentation network through an image-scale Wasserstein distance constraint, ensuring that the class ratios in the segmentation results for each unlabeled image match those predicted by the regression network. Additionally, we design a dataset-scale Wasserstein distance loss function based on a weak implicit volume prior, which enforces that the volume distribution predicted for the unlabeled dataset is similar to that of labeled dataset. Experimental results on the 2017 ACDC dataset, PROMISE12 dataset, and thigh muscle MR image dataset show the superiority of the proposed method.

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arXiv2025

SAM2-SGP: Enhancing SAM2 for Medical Image Segmentation via Support-Set Guided Prompting

Although new vision foundation models such as Segment Anything Model 2 (SAM2) have significantly enhanced zero-shot image segmentation capabilities, reliance on human-provided prompts poses significant challenges in adapting SAM2 to medical image segmentation tasks. Moreover, SAM2's performance in medical image segmentation was limited by the domain shift issue, since it was originally trained on natural images and videos. To address these challenges, we proposed SAM2 with support-set guided prompting (SAM2-SGP), a framework that eliminated the need for manual prompts. The proposed model leveraged the memory mechanism of SAM2 to generate pseudo-masks using image-mask pairs from a support set via a Pseudo-mask Generation (PMG) module. We further introduced a novel Pseudo-mask Attention (PMA) module, which used these pseudo-masks to automatically generate bounding boxes and enhance localized feature extraction by guiding attention to relevant areas. Furthermore, a low-rank adaptation (LoRA) strategy was adopted to mitigate the domain shift issue. The proposed framework was evaluated on both 2D and 3D datasets across multiple medical imaging modalities, including fundus photography, X-ray, computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasound. The results demonstrated a significant performance improvement over state-of-the-art models, such as nnUNet and SwinUNet, as well as foundation models, such as SAM2 and MedSAM2, underscoring the effectiveness of the proposed approach. Our code is publicly available at https://github.com/astlian9/SAM_Support.

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arXiv2024

RISAM: Referring Image Segmentation via Mutual-Aware Attention Features

Referring image segmentation (RIS) aims to segment a particular region based on a language expression prompt. Existing methods incorporate linguistic features into visual features and obtain multi-modal features for mask decoding. However, these methods may segment the visually salient entity instead of the correct referring region, as the multi-modal features are dominated by the abundant visual context. In this paper, we propose MARIS, a referring image segmentation method that leverages the Segment Anything Model (SAM) and introduces a mutual-aware attention mechanism to enhance the cross-modal fusion via two parallel branches. Specifically, our mutual-aware attention mechanism consists of Vision-Guided Attention and Language-Guided Attention, which bidirectionally model the relationship between visual and linguistic features. Correspondingly, we design a Mask Decoder to enable explicit linguistic guidance for more consistent segmentation with the language expression. To this end, a multi-modal query token is proposed to integrate linguistic information and interact with visual information simultaneously. Extensive experiments on three benchmark datasets show that our method outperforms the state-of-the-art RIS methods. Our code will be publicly available.

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arXiv2019

Understanding Deep Learning Techniques for Image Segmentation

The machine learning community has been overwhelmed by a plethora of deep learning based approaches. Many challenging computer vision tasks such as detection, localization, recognition and segmentation of objects in unconstrained environment are being efficiently addressed by various types of deep neural networks like convolutional neural networks, recurrent networks, adversarial networks, autoencoders and so on. While there have been plenty of analytical studies regarding the object detection or recognition domain, many new deep learning techniques have surfaced with respect to image segmentation techniques. This paper approaches these various deep learning techniques of image segmentation from an analytical perspective. The main goal of this work is to provide an intuitive understanding of the major techniques that has made significant contribution to the image segmentation domain. Starting from some of the traditional image segmentation approaches, the paper progresses describing the effect deep learning had on the image segmentation domain. Thereafter, most of the major segmentation algorithms have been logically categorized with paragraphs dedicated to their unique contribution. With an ample amount of intuitive explanations, the reader is expected to have an improved ability to visualize the internal dynamics of these processes.

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arXiv2017

Crowd Sourcing Image Segmentation with iaSTAPLE

We propose a novel label fusion technique as well as a crowdsourcing protocol to efficiently obtain accurate epithelial cell segmentations from non-expert crowd workers. Our label fusion technique simultaneously estimates the true segmentation, the performance levels of individual crowd workers, and an image segmentation model in the form of a pairwise Markov random field. We term our approach image-aware STAPLE (iaSTAPLE) since our image segmentation model seamlessly integrates into the well-known and widely used STAPLE approach. In an evaluation on a light microscopy dataset containing more than 5000 membrane labeled epithelial cells of a fly wing, we show that iaSTAPLE outperforms STAPLE in terms of segmentation accuracy as well as in terms of the accuracy of estimated crowd worker performance levels, and is able to correctly segment 99% of all cells when compared to expert segmentations. These results show that iaSTAPLE is a highly useful tool for crowd sourcing image segmentation.

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