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arXiv2025

SynthFM: Training Modality-agnostic Foundation Models for Medical Image Segmentation without Real Medical Data

Foundation models like the Segment Anything Model (SAM) excel in zero-shot segmentation for natural images but struggle with medical image segmentation due to differences in texture, contrast, and noise. Annotating medical images is costly and requires domain expertise, limiting large-scale annotated data availability. To address this, we propose SynthFM, a synthetic data generation framework that mimics the complexities of medical images, enabling foundation models to adapt without real medical data. Using SAM's pretrained encoder and training the decoder from scratch on SynthFM's dataset, we evaluated our method on 11 anatomical structures across 9 datasets (CT, MRI, and Ultrasound). SynthFM outperformed zero-shot baselines like SAM and MedSAM, achieving superior results under different prompt settings and on out-of-distribution datasets.

eess.IV↗

arXiv2010

A Q-Ising model application for linear-time image segmentation

A computational method is presented which efficiently segments digital grayscale images by directly applying the Q-state Ising (or Potts) model. Since the Potts model was first proposed in 1952, physicists have studied lattice models to gain deep insights into magnetism and other disordered systems. For some time, researchers have realized that digital images may be modeled in much the same way as these physical systems (i.e., as a square lattice of numerical values). A major drawback in using Potts model methods for image segmentation is that, with conventional methods, it processes in exponential time. Advances have been made via certain approximations to reduce the segmentation process to power-law time. However, in many applications (such as for sonar imagery), real-time processing requires much greater efficiency. This article contains a description of an energy minimization technique that applies four Potts (Q-Ising) models directly to the image and processes in linear time. The result is analogous to partitioning the system into regions of four classes of magnetism. This direct Potts segmentation technique is demonstrated on photographic, medical, and acoustic images.

physics.data-an↗

arXiv2020

U-Net and its variants for medical image segmentation: theory and applications

U-net is an image segmentation technique developed primarily for medical image analysis that can precisely segment images using a scarce amount of training data. These traits provide U-net with a very high utility within the medical imaging community and have resulted in extensive adoption of U-net as the primary tool for segmentation tasks in medical imaging. The success of U-net is evident in its widespread use in all major image modalities from CT scans and MRI to X-rays and microscopy. Furthermore, while U-net is largely a segmentation tool, there have been instances of the use of U-net in other applications. As the potential of U-net is still increasing, in this review we look at the various developments that have been made in the U-net architecture and provide observations on recent trends. We examine the various innovations that have been made in deep learning and discuss how these tools facilitate U-net. Furthermore, we look at image modalities and application areas where U-net has been applied.

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arXiv2026

XAI-CLIP: ROI-Guided Perturbation Framework for Explainable Medical Image Segmentation in Multimodal Vision-Language Models

Medical image segmentation is a critical component of clinical workflows, enabling accurate diagnosis, treatment planning, and disease monitoring. However, despite the superior performance of transformer-based models over convolutional architectures, their limited interpretability remains a major obstacle to clinical trust and deployment. Existing explainable artificial intelligence (XAI) techniques, including gradient-based saliency methods and perturbation-based approaches, are often computationally expensive, require numerous forward passes, and frequently produce noisy or anatomically irrelevant explanations. To address these limitations, we propose XAI-CLIP, an ROI-guided perturbation framework that leverages multimodal vision-language model embeddings to localize clinically meaningful anatomical regions and guide the explanation process. By integrating language-informed region localization with medical image segmentation and applying targeted, region-aware perturbations, the proposed method generates clearer, boundary-aware saliency maps while substantially reducing computational overhead. Experiments conducted on the FLARE22 and CHAOS datasets demonstrate that XAI-CLIP achieves up to a 60\% reduction in runtime, a 44.6\% improvement in dice score, and a 96.7\% increase in Intersection-over-Union for occlusion-based explanations compared to conventional perturbation methods. Qualitative results further confirm cleaner and more anatomically consistent attribution maps with fewer artifacts, highlighting that the incorporation of multimodal vision-language representations into perturbation-based XAI frameworks significantly enhances both interpretability and efficiency, thereby enabling transparent and clinically deployable medical image segmentation systems.

cs.CV↗

arXiv2021

Inconsistency-aware Uncertainty Estimation for Semi-supervised Medical Image Segmentation

In semi-supervised medical image segmentation, most previous works draw on the common assumption that higher entropy means higher uncertainty. In this paper, we investigate a novel method of estimating uncertainty. We observe that, when assigned different misclassification costs in a certain degree, if the segmentation result of a pixel becomes inconsistent, this pixel shows a relative uncertainty in its segmentation. Therefore, we present a new semi-supervised segmentation model, namely, conservative-radical network (CoraNet in short) based on our uncertainty estimation and separate self-training strategy. In particular, our CoraNet model consists of three major components: a conservative-radical module (CRM), a certain region segmentation network (C-SN), and an uncertain region segmentation network (UC-SN) that could be alternatively trained in an end-to-end manner. We have extensively evaluated our method on various segmentation tasks with publicly available benchmark datasets, including CT pancreas, MR endocardium, and MR multi-structures segmentation on the ACDC dataset. Compared with the current state of the art, our CoraNet has demonstrated superior performance. In addition, we have also analyzed its connection with and difference from conventional methods of uncertainty estimation in semi-supervised medical image segmentation.

cs.CV↗

arXiv2022

Optimizing Vision Transformers for Medical Image Segmentation

For medical image semantic segmentation (MISS), Vision Transformers have emerged as strong alternatives to convolutional neural networks thanks to their inherent ability to capture long-range correlations. However, existing research uses off-the-shelf vision Transformer blocks based on linear projections and feature processing which lack spatial and local context to refine organ boundaries. Furthermore, Transformers do not generalize well on small medical imaging datasets and rely on large-scale pre-training due to limited inductive biases. To address these problems, we demonstrate the design of a compact and accurate Transformer network for MISS, CS-Unet, which introduces convolutions in a multi-stage design for hierarchically enhancing spatial and local modeling ability of Transformers. This is mainly achieved by our well-designed Convolutional Swin Transformer (CST) block which merges convolutions with Multi-Head Self-Attention and Feed-Forward Networks for providing inherent localized spatial context and inductive biases. Experiments demonstrate CS-Unet without pre-training outperforms other counterparts by large margins on multi-organ and cardiac datasets with fewer parameters and achieves state-of-the-art performance. Our code is available at Github.

cs.CV↗

arXiv2025

CausalCLIPSeg: Unlocking CLIP's Potential in Referring Medical Image Segmentation with Causal Intervention

Referring medical image segmentation targets delineating lesions indicated by textual descriptions. Aligning visual and textual cues is challenging due to their distinct data properties. Inspired by large-scale pre-trained vision-language models, we propose CausalCLIPSeg, an end-to-end framework for referring medical image segmentation that leverages CLIP. Despite not being trained on medical data, we enforce CLIP's rich semantic space onto the medical domain by a tailored cross-modal decoding method to achieve text-to-pixel alignment. Furthermore, to mitigate confounding bias that may cause the model to learn spurious correlations instead of meaningful causal relationships, CausalCLIPSeg introduces a causal intervention module which self-annotates confounders and excavates causal features from inputs for segmentation judgments. We also devise an adversarial min-max game to optimize causal features while penalizing confounding ones. Extensive experiments demonstrate the state-of-the-art performance of our proposed method. Code is available at https://github.com/WUTCM-Lab/CausalCLIPSeg.

cs.CV↗

arXiv2025

Leveraging Labelled Data Knowledge: A Cooperative Rectification Learning Network for Semi-supervised 3D Medical Image Segmentation

Semi-supervised 3D medical image segmentation aims to achieve accurate segmentation using few labelled data and numerous unlabelled data. The main challenge in the design of semi-supervised learning methods consists in the effective use of the unlabelled data for training. A promising solution consists of ensuring consistent predictions across different views of the data, where the efficacy of this strategy depends on the accuracy of the pseudo-labels generated by the model for this consistency learning strategy. In this paper, we introduce a new methodology to produce high-quality pseudo-labels for a consistency learning strategy to address semi-supervised 3D medical image segmentation. The methodology has three important contributions. The first contribution is the Cooperative Rectification Learning Network (CRLN) that learns multiple prototypes per class to be used as external knowledge priors to adaptively rectify pseudo-labels at the voxel level. The second contribution consists of the Dynamic Interaction Module (DIM) to facilitate pairwise and cross-class interactions between prototypes and multi-resolution image features, enabling the production of accurate voxel-level clues for pseudo-label rectification. The third contribution is the Cooperative Positive Supervision (CPS), which optimises uncertain representations to align with unassertive representations of their class distributions, improving the model's accuracy in classifying uncertain regions. Extensive experiments on three public 3D medical segmentation datasets demonstrate the effectiveness and superiority of our semi-supervised learning method.

cs.CV↗

arXiv2026

Rich-U-Net: A medical image segmentation model for fusing spatial depth features and capturing minute structural details

Medical image segmentation is of great significance in analysis of illness. The use of deep neural networks in medical image segmentation can help doctors extract regions of interest from complex medical images, thereby improving diagnostic accuracy and enabling better assessment of the condition to formulate treatment plans. However, most current medical image segmentation methods underperform in accurately extracting spatial information from medical images and mining potential complex structures and variations. In this article, we introduce the Rich-U-Net model, which effectively integrates both spatial and depth features. This fusion enhances the model's capability to detect fine structures and intricate details within complex medical images. Our multi-level and multi-dimensional feature fusion and optimization strategies enable our model to achieve fine structure localization and accurate segmentation results in medical image segmentation. Experiments on the ISIC2018, BUSI, GLAS, and CVC datasets show that Rich-U-Net surpasses other state-of-the-art models in Dice, IoU, and HD95 metrics.

eess.IV↗

arXiv2023

SDC-UDA: Volumetric Unsupervised Domain Adaptation Framework for Slice-Direction Continuous Cross-Modality Medical Image Segmentation

Recent advances in deep learning-based medical image segmentation studies achieve nearly human-level performance in fully supervised manner. However, acquiring pixel-level expert annotations is extremely expensive and laborious in medical imaging fields. Unsupervised domain adaptation (UDA) can alleviate this problem, which makes it possible to use annotated data in one imaging modality to train a network that can successfully perform segmentation on target imaging modality with no labels. In this work, we propose SDC-UDA, a simple yet effective volumetric UDA framework for slice-direction continuous cross-modality medical image segmentation which combines intra- and inter-slice self-attentive image translation, uncertainty-constrained pseudo-label refinement, and volumetric self-training. Our method is distinguished from previous methods on UDA for medical image segmentation in that it can obtain continuous segmentation in the slice direction, thereby ensuring higher accuracy and potential in clinical practice. We validate SDC-UDA with multiple publicly available cross-modality medical image segmentation datasets and achieve state-of-the-art segmentation performance, not to mention the superior slice-direction continuity of prediction compared to previous studies.

cs.CV↗

arXiv2024

Enhancing Weakly-Supervised Histopathology Image Segmentation with Knowledge Distillation on MIL-Based Pseudo-Labels

Segmenting tumors in histological images is vital for cancer diagnosis. While fully supervised models excel with pixel-level annotations, creating such annotations is labor-intensive and costly. Accurate histopathology image segmentation under weakly-supervised conditions with coarse-grained image labels is still a challenging problem. Although multiple instance learning (MIL) has shown promise in segmentation tasks, surprisingly, no previous pseudo-supervision methods have used MIL-based outputs as pseudo-masks for training. We suspect this stems from concerns over noises in MIL results affecting pseudo supervision quality. To explore the potential of leveraging MIL-based segmentation for pseudo supervision, we propose a novel distillation framework for histopathology image segmentation. This framework introduces a iterative fusion-knowledge distillation strategy, enabling the student model to learn directly from the teacher's comprehensive outcomes. Through dynamic role reversal between the fixed teacher and learnable student models and the incorporation of weighted cross-entropy loss for model optimization, our approach prevents performance deterioration and noise amplification during knowledge distillation. Experimental results on public histopathology datasets, Camelyon16 and Digestpath2019, demonstrate that our approach not only complements various MIL-based segmentation methods but also significantly enhances their performance. Additionally, our method achieves new SOTA in the field.

cs.CV↗

arXiv2022

Investigating Shift-Variance of Convolutional Neural Networks in Ultrasound Image Segmentation

While accuracy is an evident criterion for ultrasound image segmentation, output consistency across different tests is equally crucial for tracking changes in regions of interest in applications such as monitoring the patients' response to treatment, measuring the progression or regression of the disease, reaching a diagnosis, or treatment planning. Convolutional neural networks (CNNs) have attracted rapidly growing interest in automatic ultrasound image segmentation recently. However, CNNs are not shift-equivariant, meaning that if the input translates, e.g., in the lateral direction by one pixel, the output segmentation may drastically change. To the best of our knowledge, this problem has not been studied in ultrasound image segmentation or even more broadly in ultrasound images. Herein, we investigate and quantify the shift-variance problem of CNNs in this application and further evaluate the performance of a recently published technique, called BlurPooling, for addressing the problem. In addition, we propose the Pyramidal BlurPooling method that outperforms BlurPooling in both output consistency and segmentation accuracy. Finally, we demonstrate that data augmentation is not a replacement for the proposed method. Source code is available at https://git.io/pbpunet and http://code.sonography.ai.

eess.IV↗

arXiv2024

Deep evidential fusion with uncertainty quantification and contextual discounting for multimodal medical image segmentation

Single-modality medical images generally do not contain enough information to reach an accurate and reliable diagnosis. For this reason, physicians generally diagnose diseases based on multimodal medical images such as, e.g., PET/CT. The effective fusion of multimodal information is essential to reach a reliable decision and explain how the decision is made as well. In this paper, we propose a fusion framework for multimodal medical image segmentation based on deep learning and the Dempster-Shafer theory of evidence. In this framework, the reliability of each single modality image when segmenting different objects is taken into account by a contextual discounting operation. The discounted pieces of evidence from each modality are then combined by Dempster's rule to reach a final decision. Experimental results with a PET-CT dataset with lymphomas and a multi-MRI dataset with brain tumors show that our method outperforms the state-of-the-art methods in accuracy and reliability.

eess.IV↗

arXiv2026

VCDP: Variation-Conditioned Distributional Proxy Learning for Semi-Supervised Medical Image Segmentation

Semi-supervised 3D medical image segmentation reduces the need for dense voxel-level annotations by exploiting unlabeled volumes. Although existing methods such as consistency regularization, pseudo-labeling, and co-training improve prediction-level robustness, they often provide insufficient feature-space organization for anatomically complex structures, especially small organs and ambiguous boundary regions with large intra-class variations. To address this issue, we propose Variation-Conditioned Distributional Proxy Learning (VCDP), a plug-and-play training-only regularization module for semi-supervised 3D medical image segmentation. VCDP represents each class with a learnable Gaussian distribution for shared class semantics and multiple variation prototypes for fine-grained intra-class patterns. A unified variation-conditioned compatibility score is further formulated to fuse distributional similarity and soft variation aggregation, guiding voxel embeddings to align with both global organ identity and local anatomical variations. VCDP is attached to decoder features during training and removed during inference, introducing no additional inference cost. Experiments on multi-organ segmentation benchmarks show that VCDP improves most evaluated baselines, particularly for small, ambiguous, and highly variable organs. Our anonymous code is released at https://anonymous.4open.science/r/VCDP_code-41ED.

cs.CV↗

arXiv2023

Bidirectional Copy-Paste for Semi-Supervised Medical Image Segmentation

In semi-supervised medical image segmentation, there exist empirical mismatch problems between labeled and unlabeled data distribution. The knowledge learned from the labeled data may be largely discarded if treating labeled and unlabeled data separately or in an inconsistent manner. We propose a straightforward method for alleviating the problem - copy-pasting labeled and unlabeled data bidirectionally, in a simple Mean Teacher architecture. The method encourages unlabeled data to learn comprehensive common semantics from the labeled data in both inward and outward directions. More importantly, the consistent learning procedure for labeled and unlabeled data can largely reduce the empirical distribution gap. In detail, we copy-paste a random crop from a labeled image (foreground) onto an unlabeled image (background) and an unlabeled image (foreground) onto a labeled image (background), respectively. The two mixed images are fed into a Student network and supervised by the mixed supervisory signals of pseudo-labels and ground-truth. We reveal that the simple mechanism of copy-pasting bidirectionally between labeled and unlabeled data is good enough and the experiments show solid gains (e.g., over 21% Dice improvement on ACDC dataset with 5% labeled data) compared with other state-of-the-arts on various semi-supervised medical image segmentation datasets. Code is available at https://github.com/DeepMed-Lab-ECNU/BCP}.

cs.CV↗

arXiv2020

Simple Interactive Image Segmentation using Label Propagation through kNN graphs

Many interactive image segmentation techniques are based on semi-supervised learning. The user may label some pixels from each object and the SSL algorithm will propagate the labels from the labeled to the unlabeled pixels, finding object boundaries. This paper proposes a new SSL graph-based interactive image segmentation approach, using undirected and unweighted kNN graphs, from which the unlabeled nodes receive contributions from other nodes (either labeled or unlabeled). It is simpler than many other techniques, but it still achieves significant classification accuracy in the image segmentation task. Computer simulations are performed using some real-world images, extracted from the Microsoft GrabCut dataset. The segmentation results show the effectiveness of the proposed approach.

cs.LG↗

arXiv2021

InfoSeg: Unsupervised Semantic Image Segmentation with Mutual Information Maximization

We propose a novel method for unsupervised semantic image segmentation based on mutual information maximization between local and global high-level image features. The core idea of our work is to leverage recent progress in self-supervised image representation learning. Representation learning methods compute a single high-level feature capturing an entire image. In contrast, we compute multiple high-level features, each capturing image segments of one particular semantic class. To this end, we propose a novel two-step learning procedure comprising a segmentation and a mutual information maximization step. In the first step, we segment images based on local and global features. In the second step, we maximize the mutual information between local features and high-level features of their respective class. For training, we provide solely unlabeled images and start from random network initialization. For quantitative and qualitative evaluation, we use established benchmarks, and COCO-Persons, whereby we introduce the latter in this paper as a challenging novel benchmark. InfoSeg significantly outperforms the current state-of-the-art, e.g., we achieve a relative increase of 26% in the Pixel Accuracy metric on the COCO-Stuff dataset.

cs.CV↗

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.

cs.CV↗