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arXiv2023

Semantic Image Segmentation: Two Decades of Research

Semantic image segmentation (SiS) plays a fundamental role in a broad variety of computer vision applications, providing key information for the global understanding of an image. This survey is an effort to summarize two decades of research in the field of SiS, where we propose a literature review of solutions starting from early historical methods followed by an overview of more recent deep learning methods including the latest trend of using transformers. We complement the review by discussing particular cases of the weak supervision and side machine learning techniques that can be used to improve the semantic segmentation such as curriculum, incremental or self-supervised learning. State-of-the-art SiS models rely on a large amount of annotated samples, which are more expensive to obtain than labels for tasks such as image classification. Since unlabeled data is instead significantly cheaper to obtain, it is not surprising that Unsupervised Domain Adaptation (UDA) reached a broad success within the semantic segmentation community. Therefore, a second core contribution of this book is to summarize five years of a rapidly growing field, Domain Adaptation for Semantic Image Segmentation (DASiS) which embraces the importance of semantic segmentation itself and a critical need of adapting segmentation models to new environments. In addition to providing a comprehensive survey on DASiS techniques, we unveil also newer trends such as multi-domain learning, domain generalization, domain incremental learning, test-time adaptation and source-free domain adaptation. Finally, we conclude this survey by describing datasets and benchmarks most widely used in SiS and DASiS and briefly discuss related tasks such as instance and panoptic image segmentation, as well as applications such as medical image segmentation.

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arXiv2025

Bidirectional Uncertainty-Aware Region Learning for Semi-Supervised Medical Image Segmentation

In semi-supervised medical image segmentation, the poor quality of unlabeled data and the uncertainty in the model's predictions lead to models that inevitably produce erroneous pseudo-labels. These errors accumulate throughout model training, thereby weakening the model's performance. We found that these erroneous pseudo-labels are typically concentrated in high-uncertainty regions. Traditional methods improve performance by directly discarding pseudo-labels in these regions, which can also result in neglecting potentially valuable training data. To alleviate this problem, we propose a bidirectional uncertainty-aware region learning strategy to fully utilize the precise supervision provided by labeled data and stabilize the training of unlabeled data. Specifically, in the training labeled data, we focus on high-uncertainty regions, using precise label information to guide the model's learning in potentially uncontrollable areas. Meanwhile, in the training of unlabeled data, we concentrate on low-uncertainty regions to reduce the interference of erroneous pseudo-labels on the model. Through this bidirectional learning strategy, the model's overall performance has significantly improved. Extensive experiments show that our proposed method achieves significant performance improvement on different medical image segmentation tasks.

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arXiv2025

Evaluation framework for Image Segmentation Algorithms

This paper presents a comprehensive evaluation framework for image segmentation algorithms, encompassing naive methods, machine learning approaches, and deep learning techniques. We begin by introducing the fundamental concepts and importance of image segmentation, and the role of interactive segmentation in enhancing accuracy. A detailed background theory section explores various segmentation methods, including thresholding, edge detection, region growing, feature extraction, random forests, support vector machines, convolutional neural networks, U-Net, and Mask R-CNN. The implementation and experimental setup are thoroughly described, highlighting three primary approaches: algorithm assisting user, user assisting algorithm, and hybrid methods. Evaluation metrics such as Intersection over Union (IoU), computation time, and user interaction time are employed to measure performance. A comparative analysis presents detailed results, emphasizing the strengths, limitations, and trade-offs of each method. The paper concludes with insights into the practical applicability of these approaches across various scenarios and outlines future work, focusing on expanding datasets, developing more representative approaches, integrating real-time feedback, and exploring weakly supervised and self-supervised learning paradigms to enhance segmentation accuracy and efficiency. Keywords: Image Segmentation, Interactive Segmentation, Machine Learning, Deep Learning, Computer Vision

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arXiv2021

Color image segmentation based on a convex K-means approach

Image segmentation is a fundamental and challenging task in image processing and computer vision. The color image segmentation is attracting more attention due to the color image provides more information than the gray image. In this paper, we propose a variational model based on a convex K-means approach to segment color images. The proposed variational method uses a combination of $l_1$ and $l_2$ regularizers to maintain edge information of objects in images while overcoming the staircase effect. Meanwhile, our one-stage strategy is an improved version based on the smoothing and thresholding strategy, which contributes to improving the accuracy of segmentation. The proposed method performs the following steps. First, we specify the color set which can be determined by human or the K-means method. Second, we use a variational model to obtain the most appropriate color for each pixel from the color set via convex relaxation and lifting. The Chambolle-Pock algorithm and simplex projection are applied to solve the variational model effectively. Experimental results and comparison analysis demonstrate the effectiveness and robustness of our method.

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arXiv2023

Multi Task Consistency Guided Source-Free Test-Time Domain Adaptation Medical Image Segmentation

Source-free test-time adaptation for medical image segmentation aims to enhance the adaptability of segmentation models to diverse and previously unseen test sets of the target domain, which contributes to the generalizability and robustness of medical image segmentation models without access to the source domain. Ensuring consistency between target edges and paired inputs is crucial for test-time adaptation. To improve the performance of test-time domain adaptation, we propose a multi task consistency guided source-free test-time domain adaptation medical image segmentation method which ensures the consistency of the local boundary predictions and the global prototype representation. Specifically, we introduce a local boundary consistency constraint method that explores the relationship between tissue region segmentation and tissue boundary localization tasks. Additionally, we propose a global feature consistency constraint toto enhance the intra-class compactness. We conduct extensive experiments on the segmentation of benchmark fundus images. Compared to prediction directly by the source domain model, the segmentation Dice score is improved by 6.27\% and 0.96\% in RIM-ONE-r3 and Drishti GS datasets, respectively. Additionally, the results of experiments demonstrate that our proposed method outperforms existing competitive domain adaptation segmentation algorithms.

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arXiv2025

Concentrate on Weakness: Mining Hard Prototypes for Few-Shot Medical Image Segmentation

Few-Shot Medical Image Segmentation (FSMIS) has been widely used to train a model that can perform segmentation from only a few annotated images. However, most existing prototype-based FSMIS methods generate multiple prototypes from the support image solely by random sampling or local averaging, which can cause particularly severe boundary blurring due to the tendency for normal features accounting for the majority of features of a specific category. Consequently, we propose to focus more attention to those weaker features that are crucial for clear segmentation boundary. Specifically, we design a Support Self-Prediction (SSP) module to identify such weak features by comparing true support mask with one predicted by global support prototype. Then, a Hard Prototypes Generation (HPG) module is employed to generate multiple hard prototypes based on these weak features. Subsequently, a Multiple Similarity Maps Fusion (MSMF) module is devised to generate final segmenting mask in a dual-path fashion to mitigate the imbalance between foreground and background in medical images. Furthermore, we introduce a boundary loss to further constraint the edge of segmentation. Extensive experiments on three publicly available medical image datasets demonstrate that our method achieves state-of-the-art performance. Code is available at https://github.com/jcjiang99/CoW.

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arXiv2020

Unsupervised Image Segmentation using Mutual Mean-Teaching

Unsupervised image segmentation aims at assigning the pixels with similar feature into a same cluster without annotation, which is an important task in computer vision. Due to lack of prior knowledge, most of existing model usually need to be trained several times to obtain suitable results. To address this problem, we propose an unsupervised image segmentation model based on the Mutual Mean-Teaching (MMT) framework to produce more stable results. In addition, since the labels of pixels from two model are not matched, a label alignment algorithm based on the Hungarian algorithm is proposed to match the cluster labels. Experimental results demonstrate that the proposed model is able to segment various types of images and achieves better performance than the existing methods.

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arXiv2021

Distributing Deep Learning Hyperparameter Tuning for 3D Medical Image Segmentation

Most research on novel techniques for 3D Medical Image Segmentation (MIS) is currently done using Deep Learning with GPU accelerators. The principal challenge of such technique is that a single input can easily cope computing resources, and require prohibitive amounts of time to be processed. Distribution of deep learning and scalability over computing devices is an actual need for progressing on such research field. Conventional distribution of neural networks consist in data parallelism, where data is scattered over resources (e.g., GPUs) to parallelize the training of the model. However, experiment parallelism is also an option, where different training processes are parallelized across resources. While the first option is much more common on 3D image segmentation, the second provides a pipeline design with less dependence among parallelized processes, allowing overhead reduction and more potential scalability. In this work we present a design for distributed deep learning training pipelines, focusing on multi-node and multi-GPU environments, where the two different distribution approaches are deployed and benchmarked. We take as proof of concept the 3D U-Net architecture, using the MSD Brain Tumor Segmentation dataset, a state-of-art problem in medical image segmentation with high computing and space requirements. Using the BSC MareNostrum supercomputer as benchmarking environment, we use TensorFlow and Ray as neural network training and experiment distribution platforms. We evaluate the experiment speed-up, showing the potential for scaling out on GPUs and nodes. Also comparing the different parallelism techniques, showing how experiment distribution leverages better such resources through scaling. Finally, we provide the implementation of the design open to the community, and the non-trivial steps and methodology for adapting and deploying a MIS case as the here presented.

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arXiv2020

Deep learning for image segmentation: veritable or overhyped?

Deep learning has achieved great success as a powerful classification tool and also made great progress in sematic segmentation. As a result, many researchers also believe that deep learning is the most powerful tool for pixel level image segmentation. Could deep learning achieve the same pixel level accuracy as traditional image segmentation techniques by mapping the features of the object into a non-linear function? This paper gives a short survey of the accuracies achieved by deep learning so far in image classification and image segmentation. Compared to the high accuracies achieved by deep learning in classifying limited categories in international vision challenges, the image segmentation accuracies achieved by deep learning in the same challenges are only about eighty percent. On the contrary, the image segmentation accuracies achieved in international biomedical challenges are close to ninty five percent. Why the difference is so big? Since the accuracies of the competitors methods are only evaluated based on their submitted results instead of reproducing the results by submitting the source codes or the software, are the achieved accuracies verifiable or overhyped? We are going to find it out by analyzing the working principle of deep learning. Finally, we compared the accuracies of state of the art deep learning methods with a threshold selection method quantitatively. Experimental results showed that the threshold selection method could achieve significantly higher accuracy than deep learning methods in image segmentation.

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arXiv2022

TransAttUnet: Multi-level Attention-guided U-Net with Transformer for Medical Image Segmentation

Accurate segmentation of organs or lesions from medical images is crucial for reliable diagnosis of diseases and organ morphometry. In recent years, convolutional encoder-decoder solutions have achieved substantial progress in the field of automatic medical image segmentation. Due to the inherent bias in the convolution operations, prior models mainly focus on local visual cues formed by the neighboring pixels, but fail to fully model the long-range contextual dependencies. In this paper, we propose a novel Transformer-based Attention Guided Network called TransAttUnet, in which the multi-level guided attention and multi-scale skip connection are designed to jointly enhance the performance of the semantical segmentation architecture. Inspired by Transformer, the self-aware attention (SAA) module with Transformer Self Attention (TSA) and Global Spatial Attention (GSA) is incorporated into TransAttUnet to effectively learn the non-local interactions among encoder features. Moreover, we also use additional multi-scale skip connections between decoder blocks to aggregate the upsampled features with different semantic scales. In this way, the representation ability of multi-scale context information is strengthened to generate discriminative features. Benefitting from these complementary components, the proposed TransAttUnet can effectively alleviate the loss of fine details caused by the stacking of convolution layers and the consecutive sampling operations, finally improving the segmentation quality of medical images. Extensive experiments on multiple medical image segmentation datasets from different imaging modalities demonstrate that the proposed method consistently outperforms the state-of-the-art baselines. Our code and pre-trained models are available at: https://github.com/YishuLiu/TransAttUnet.

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arXiv2021

Dual-Task Mutual Learning for Semi-Supervised Medical Image Segmentation

The success of deep learning methods in medical image segmentation tasks usually requires a large amount of labeled data. However, obtaining reliable annotations is expensive and time-consuming. Semi-supervised learning has attracted much attention in medical image segmentation by taking the advantage of unlabeled data which is much easier to acquire. In this paper, we propose a novel dual-task mutual learning framework for semi-supervised medical image segmentation. Our framework can be formulated as an integration of two individual segmentation networks based on two tasks: learning region-based shape constraint and learning boundary-based surface mismatch. Different from the one-way transfer between teacher and student networks, an ensemble of dual-task students can learn collaboratively and implicitly explore useful knowledge from each other during the training process. By jointly learning the segmentation probability maps and signed distance maps of targets, our framework can enforce the geometric shape constraint and learn more reliable information. Experimental results demonstrate that our method achieves performance gains by leveraging unlabeled data and outperforms the state-of-the-art semi-supervised segmentation methods.

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arXiv2026

RIS-FUSION: Rethinking Text-Driven Infrared and Visible Image Fusion from the Perspective of Referring Image Segmentation

Text-driven infrared and visible image fusion has gained attention for enabling natural language to guide the fusion process. However, existing methods lack a goal-aligned task to supervise and evaluate how effectively the input text contributes to the fusion outcome. We observe that referring image segmentation (RIS) and text-driven fusion share a common objective: highlighting the object referred to by the text. Motivated by this, we propose RIS-FUSION, a cascaded framework that unifies fusion and RIS through joint optimization. At its core is the LangGatedFusion module, which injects textual features into the fusion backbone to enhance semantic alignment. To support multimodal referring image segmentation task, we introduce MM-RIS, a large-scale benchmark with 12.5k training and 3.5k testing triplets, each consisting of an infrared-visible image pair, a segmentation mask, and a referring expression. Extensive experiments show that RIS-FUSION achieves state-of-the-art performance, outperforming existing methods by over 11% in mIoU. Code and dataset will be released at https://github.com/SijuMa2003/RIS-FUSION.

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arXiv2025

Advanced Image Segmentation Techniques for Neural Activity Detection via C-fos Immediate Early Gene Expression

This paper investigates the application of advanced image segmentation techniques to analyze C-fos immediate early gene expression, a crucial marker for neural activity. Due to the complexity and high variability of neural circuits, accurate segmentation of C-fos images is paramount for the development of new insights into neural function. Amidst this backdrop, this research aims to improve accuracy and minimize manual intervention in C-fos image segmentation by leveraging the capabilities of CNNs and the Unet model. We describe the development of a novel workflow for the segmentation process involving Convolutional Neural Networks (CNNs) and the Unet model, demonstrating their efficiency in various image segmentation tasks. Our workflow incorporates pre-processing steps such as cropping, image feature extraction, and clustering for the training dataset selection. We used an AutoEncoder model to extract features and implement constrained clustering to identify similarities and differences in image types. Additionally, we utilized manual and automatic labeling approaches to enhance the performance of our model. We demonstrated the effectiveness of our method in distinguishing areas with significant C-fos expression from normal tissue areas. Lastly, we implemented a modified Unet network for the detection of C-fos expressions. This research contributes to the development of more efficient and automated image segmentation methods, advancing the understanding of neural function in neuroscience research.

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arXiv2024

Medical Image Segmentation with InTEnt: Integrated Entropy Weighting for Single Image Test-Time Adaptation

Test-time adaptation (TTA) refers to adapting a trained model to a new domain during testing. Existing TTA techniques rely on having multiple test images from the same domain, yet this may be impractical in real-world applications such as medical imaging, where data acquisition is expensive and imaging conditions vary frequently. Here, we approach such a task, of adapting a medical image segmentation model with only a single unlabeled test image. Most TTA approaches, which directly minimize the entropy of predictions, fail to improve performance significantly in this setting, in which we also observe the choice of batch normalization (BN) layer statistics to be a highly important yet unstable factor due to only having a single test domain example. To overcome this, we propose to instead integrate over predictions made with various estimates of target domain statistics between the training and test statistics, weighted based on their entropy statistics. Our method, validated on 24 source/target domain splits across 3 medical image datasets surpasses the leading method by 2.9% Dice coefficient on average.

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arXiv2024

GraphCL: Graph-based Clustering for Semi-Supervised Medical Image Segmentation

Semi-supervised learning (SSL) has made notable advancements in medical image segmentation (MIS), particularly in scenarios with limited labeled data and significantly enhancing data utilization efficiency. Previous methods primarily focus on complex training strategies to utilize unlabeled data but neglect the importance of graph structural information. Different from existing methods, we propose a graph-based clustering for semi-supervised medical image segmentation (GraphCL) by jointly modeling graph data structure in a unified deep model. The proposed GraphCL model enjoys several advantages. Firstly, to the best of our knowledge, this is the first work to model the data structure information for semi-supervised medical image segmentation (SSMIS). Secondly, to get the clustered features across different graphs, we integrate both pairwise affinities between local image features and raw features as inputs. Extensive experimental results on three standard benchmarks show that the proposed GraphCL algorithm outperforms state-of-the-art semi-supervised medical image segmentation methods.

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arXiv2024

ConDSeg: A General Medical Image Segmentation Framework via Contrast-Driven Feature Enhancement

Medical image segmentation plays an important role in clinical decision making, treatment planning, and disease tracking. However, it still faces two major challenges. On the one hand, there is often a ``soft boundary'' between foreground and background in medical images, with poor illumination and low contrast further reducing the distinguishability of foreground and background within the image. On the other hand, co-occurrence phenomena are widespread in medical images, and learning these features is misleading to the model's judgment. To address these challenges, we propose a general framework called Contrast-Driven Medical Image Segmentation (ConDSeg). First, we develop a contrastive training strategy called Consistency Reinforcement. It is designed to improve the encoder's robustness in various illumination and contrast scenarios, enabling the model to extract high-quality features even in adverse environments. Second, we introduce a Semantic Information Decoupling module, which is able to decouple features from the encoder into foreground, background, and uncertainty regions, gradually acquiring the ability to reduce uncertainty during training. The Contrast-Driven Feature Aggregation module then contrasts the foreground and background features to guide multi-level feature fusion and key feature enhancement, further distinguishing the entities to be segmented. We also propose a Size-Aware Decoder to solve the scale singularity of the decoder. It accurately locate entities of different sizes in the image, thus avoiding erroneous learning of co-occurrence features. Extensive experiments on five medical image datasets across three scenarios demonstrate the state-of-the-art performance of our method, proving its advanced nature and general applicability to various medical image segmentation scenarios. Our released code is available at \url{https://github.com/Mengqi-Lei/ConDSeg}.

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arXiv2023

PCDAL: A Perturbation Consistency-Driven Active Learning Approach for Medical Image Segmentation and Classification

In recent years, deep learning has become a breakthrough technique in assisting medical image diagnosis. Supervised learning using convolutional neural networks (CNN) provides state-of-the-art performance and has served as a benchmark for various medical image segmentation and classification. However, supervised learning deeply relies on large-scale annotated data, which is expensive, time-consuming, and even impractical to acquire in medical imaging applications. Active Learning (AL) methods have been widely applied in natural image classification tasks to reduce annotation costs by selecting more valuable examples from the unlabeled data pool. However, their application in medical image segmentation tasks is limited, and there is currently no effective and universal AL-based method specifically designed for 3D medical image segmentation. To address this limitation, we propose an AL-based method that can be simultaneously applied to 2D medical image classification, segmentation, and 3D medical image segmentation tasks. We extensively validated our proposed active learning method on three publicly available and challenging medical image datasets, Kvasir Dataset, COVID-19 Infection Segmentation Dataset, and BraTS2019 Dataset. The experimental results demonstrate that our PCDAL can achieve significantly improved performance with fewer annotations in 2D classification and segmentation and 3D segmentation tasks. The codes of this study are available at https://github.com/ortonwang/PCDAL.

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arXiv2026

Decoding Matters: Efficient Mamba-Based Decoder with Distribution-Aware Deep Supervision for Medical Image Segmentation

Deep learning has achieved remarkable success in medical image segmentation, often reaching expert-level accuracy in delineating tumors and tissues. However, most existing approaches remain task-specific, showing strong performance on individual datasets but limited generalization across diverse imaging modalities. Moreover, many methods focus primarily on the encoder, relying on large pretrained backbones that increase computational complexity. In this paper, we propose a decoder-centric approach for generalized 2D medical image segmentation. The proposed Deco-Mamba follows a U-Net-like structure with a Transformer-CNN-Mamba design. The encoder combines a CNN block and Transformer backbone for efficient feature extraction, while the decoder integrates our novel Co-Attention Gate (CAG), Vision State Space Module (VSSM), and deformable convolutional refinement block to enhance multi-scale contextual representation. Additionally, a windowed distribution-aware KL-divergence loss is introduced for deep supervision across multiple decoding stages. Extensive experiments on diverse medical image segmentation benchmarks yield state-of-the-art performance and strong generalization capability while maintaining moderate model complexity. The source code will be released upon acceptance.

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