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arXiv2018

TernausNet: U-Net with VGG11 Encoder Pre-Trained on ImageNet for Image Segmentation

Pixel-wise image segmentation is demanding task in computer vision. Classical U-Net architectures composed of encoders and decoders are very popular for segmentation of medical images, satellite images etc. Typically, neural network initialized with weights from a network pre-trained on a large data set like ImageNet shows better performance than those trained from scratch on a small dataset. In some practical applications, particularly in medicine and traffic safety, the accuracy of the models is of utmost importance. In this paper, we demonstrate how the U-Net type architecture can be improved by the use of the pre-trained encoder. Our code and corresponding pre-trained weights are publicly available at https://github.com/ternaus/TernausNet. We compare three weight initialization schemes: LeCun uniform, the encoder with weights from VGG11 and full network trained on the Carvana dataset. This network architecture was a part of the winning solution (1st out of 735) in the Kaggle: Carvana Image Masking Challenge.

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arXiv2022

Segmentation Ability Map: Interpret deep features for medical image segmentation

Deep convolutional neural networks (CNNs) have been widely used for medical image segmentation. In most studies, only the output layer is exploited to compute the final segmentation results and the hidden representations of the deep learned features have not been well understood. In this paper, we propose a prototype segmentation (ProtoSeg) method to compute a binary segmentation map based on deep features. We measure the segmentation abilities of the features by computing the Dice between the feature segmentation map and ground-truth, named as the segmentation ability score (SA score for short). The corresponding SA score can quantify the segmentation abilities of deep features in different layers and units to understand the deep neural networks for segmentation. In addition, our method can provide a mean SA score which can give a performance estimation of the output on the test images without ground-truth. Finally, we use the proposed ProtoSeg method to compute the segmentation map directly on input images to further understand the segmentation ability of each input image. Results are presented on segmenting tumors in brain MRI, lesions in skin images, COVID-related abnormality in CT images, prostate segmentation in abdominal MRI, and pancreatic mass segmentation in CT images. Our method can provide new insights for interpreting and explainable AI systems for medical image segmentation. Our code is available on: \url{https://github.com/shengfly/ProtoSeg}.

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arXiv2020

Confidence Calibration and Predictive Uncertainty Estimation for Deep Medical Image Segmentation

Fully convolutional neural networks (FCNs), and in particular U-Nets, have achieved state-of-the-art results in semantic segmentation for numerous medical imaging applications. Moreover, batch normalization and Dice loss have been used successfully to stabilize and accelerate training. However, these networks are poorly calibrated i.e. they tend to produce overconfident predictions both in correct and erroneous classifications, making them unreliable and hard to interpret. In this paper, we study predictive uncertainty estimation in FCNs for medical image segmentation. We make the following contributions: 1) We systematically compare cross entropy loss with Dice loss in terms of segmentation quality and uncertainty estimation of FCNs; 2) We propose model ensembling for confidence calibration of the FCNs trained with batch normalization and Dice loss; 3) We assess the ability of calibrated FCNs to predict segmentation quality of structures and detect out-of-distribution test examples. We conduct extensive experiments across three medical image segmentation applications of the brain, the heart, and the prostate to evaluate our contributions. The results of this study offer considerable insight into the predictive uncertainty estimation and out-of-distribution detection in medical image segmentation and provide practical recipes for confidence calibration. Moreover, we consistently demonstrate that model ensembling improves confidence calibration.

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arXiv2025

Spatial-aware Symmetric Alignment for Text-guided Medical Image Segmentation

Text-guided Medical Image Segmentation has shown considerable promise for medical image segmentation, with rich clinical text serving as an effective supplement for scarce data. However, current methods have two key bottlenecks. On one hand, they struggle to process diagnostic and descriptive texts simultaneously, making it difficult to identify lesions and establish associations with image regions. On the other hand, existing approaches focus on lesions description and fail to capture positional constraints, leading to critical deviations. Specifically, with the text "in the left lower lung", the segmentation results may incorrectly cover both sides of the lung. To address the limitations, we propose the Spatial-aware Symmetric Alignment (SSA) framework to enhance the capacity of referring hybrid medical texts consisting of locational, descriptive, and diagnostic information. Specifically, we propose symmetric optimal transport alignment mechanism to strengthen the associations between image regions and multiple relevant expressions, which establishes bi-directional fine-grained multimodal correspondences. In addition, we devise a composite directional guidance strategy that explicitly introduces spatial constraints in the text by constructing region-level guidance masks. Extensive experiments on public benchmarks demonstrate that SSA achieves state-of-the-art (SOTA) performance, particularly in accurately segmenting lesions characterized by spatial relational constraints.

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arXiv2023

Semi-Supervised Medical Image Segmentation with Co-Distribution Alignment

Medical image segmentation has made significant progress when a large amount of labeled data are available. However, annotating medical image segmentation datasets is expensive due to the requirement of professional skills. Additionally, classes are often unevenly distributed in medical images, which severely affects the classification performance on minority classes. To address these problems, this paper proposes Co-Distribution Alignment (Co-DA) for semi-supervised medical image segmentation. Specifically, Co-DA aligns marginal predictions on unlabeled data to marginal predictions on labeled data in a class-wise manner with two differently initialized models before using the pseudo-labels generated by one model to supervise the other. Besides, we design an over-expectation cross-entropy loss for filtering the unlabeled pixels to reduce noise in their pseudo-labels. Quantitative and qualitative experiments on three public datasets demonstrate that the proposed approach outperforms existing state-of-the-art semi-supervised medical image segmentation methods on both the 2D CaDIS dataset and the 3D LGE-MRI and ACDC datasets, achieving an mIoU of 0.8515 with only 24% labeled data on CaDIS, and a Dice score of 0.8824 and 0.8773 with only 20% data on LGE-MRI and ACDC, respectively.

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arXiv2023

SAM Fails to Segment Anything? -- SAM-Adapter: Adapting SAM in Underperformed Scenes: Camouflage, Shadow, Medical Image Segmentation, and More

The emergence of large models, also known as foundation models, has brought significant advancements to AI research. One such model is Segment Anything (SAM), which is designed for image segmentation tasks. However, as with other foundation models, our experimental findings suggest that SAM may fail or perform poorly in certain segmentation tasks, such as shadow detection and camouflaged object detection (concealed object detection). This study first paves the way for applying the large pre-trained image segmentation model SAM to these downstream tasks, even in situations where SAM performs poorly. Rather than fine-tuning the SAM network, we propose \textbf{SAM-Adapter}, which incorporates domain-specific information or visual prompts into the segmentation network by using simple yet effective adapters. By integrating task-specific knowledge with general knowledge learnt by the large model, SAM-Adapter can significantly elevate the performance of SAM in challenging tasks as shown in extensive experiments. We can even outperform task-specific network models and achieve state-of-the-art performance in the task we tested: camouflaged object detection, shadow detection. We also tested polyp segmentation (medical image segmentation) and achieves better results. We believe our work opens up opportunities for utilizing SAM in downstream tasks, with potential applications in various fields, including medical image processing, agriculture, remote sensing, and more.

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arXiv2026

Reliability-Role Collaborative Learning for Semi-Supervised Cardiac Image Segmentation

Semi-supervised cardiac image segmentation aims to exploit abundant unlabeled images together with limited annotations, but the reliability of pseudo-label supervision is highly uneven across spatial regions. In a dual-network setting, interior regions are usually more stable, whereas boundary regions, low-confidence areas, and disagreements between networks can introduce noisy supervision. However, existing methods typically impose uniform supervision on all unlabeled pixels, overlooking reliability differences and limiting discriminative learning in challenging areas. To address this issue, we propose R2CL (Reliability-Role Collaborative Learning), a framework for semi-supervised cardiac image segmentation. R2CL models confidence relationships between two networks to assign roles to unlabeled regions: mutually uncertain regions are used for entropy regularization, confidence-discrepant regions for directional knowledge transfer, and mutually confident regions as reliable supervision anchors. Reliability-Role Mixed Cross Learning (RR-MCL) implements these roles through region-mixed training, directional cross-network supervision, and entropy regularization over mutually uncertain regions. Reliability-Transition Prototype Contrastive Learning (RT-PCL) constructs query features from foreground-adjacent reliability-transition regions and learns network-specific class prototypes from mutually confident regions, improving feature discrimination around ambiguous boundaries. High-confidence Context Refinement (HCR) exploits reliable interior pixels and trusted dense blocks within mutually confident regions to complement stable contextual supervision. R2CL achieves stable improvements in region-overlap and boundary-related metrics across multiple datasets, with more evident advantages on the foreground-sparse MVAA-CT dataset.

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arXiv2010

A New Approach to Lung Image Segmentation using Fuzzy Possibilistic C-Means Algorithm

Image segmentation is a vital part of image processing. Segmentation has its application widespread in the field of medical images in order to diagnose curious diseases. The same medical images can be segmented manually. But the accuracy of image segmentation using the segmentation algorithms is more when compared with the manual segmentation. In the field of medical diagnosis an extensive diversity of imaging techniques is presently available, such as radiography, computed tomography (CT) and magnetic resonance imaging (MRI). Medical image segmentation is an essential step for most consequent image analysis tasks. Although the original FCM algorithm yields good results for segmenting noise free images, it fails to segment images corrupted by noise, outliers and other imaging artifact. This paper presents an image segmentation approach using Modified Fuzzy C-Means (FCM) algorithm and Fuzzy Possibilistic c-means algorithm (FPCM). This approach is a generalized version of standard Fuzzy CMeans Clustering (FCM) algorithm. The limitation of the conventional FCM technique is eliminated in modifying the standard technique. The Modified FCM algorithm is formulated by modifying the distance measurement of the standard FCM algorithm to permit the labeling of a pixel to be influenced by other pixels and to restrain the noise effect during segmentation. Instead of having one term in the objective function, a second term is included, forcing the membership to be as high as possible without a maximum limit constraint of one. Experiments are conducted on real images to investigate the performance of the proposed modified FCM technique in segmenting the medical images. Standard FCM, Modified FCM, Fuzzy Possibilistic CMeans algorithm (FPCM) are compared to explore the accuracy of our proposed approach.

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arXiv2020

Embracing Imperfect Datasets: A Review of Deep Learning Solutions for Medical Image Segmentation

The medical imaging literature has witnessed remarkable progress in high-performing segmentation models based on convolutional neural networks. Despite the new performance highs, the recent advanced segmentation models still require large, representative, and high quality annotated datasets. However, rarely do we have a perfect training dataset, particularly in the field of medical imaging, where data and annotations are both expensive to acquire. Recently, a large body of research has studied the problem of medical image segmentation with imperfect datasets, tackling two major dataset limitations: scarce annotations where only limited annotated data is available for training, and weak annotations where the training data has only sparse annotations, noisy annotations, or image-level annotations. In this article, we provide a detailed review of the solutions above, summarizing both the technical novelties and empirical results. We further compare the benefits and requirements of the surveyed methodologies and provide our recommended solutions. We hope this survey article increases the community awareness of the techniques that are available to handle imperfect medical image segmentation datasets.

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arXiv2018

Unsupervised Pathology Image Segmentation Using Representation Learning with Spherical K-means

This paper presents a novel method for unsupervised segmentation of pathology images. Staging of lung cancer is a major factor of prognosis. Measuring the maximum dimensions of the invasive component in a pathology images is an essential task. Therefore, image segmentation methods for visualizing the extent of invasive and noninvasive components on pathology images could support pathological examination. However, it is challenging for most of the recent segmentation methods that rely on supervised learning to cope with unlabeled pathology images. In this paper, we propose a unified approach to unsupervised representation learning and clustering for pathology image segmentation. Our method consists of two phases. In the first phase, we learn feature representations of training patches from a target image using the spherical k-means. The purpose of this phase is to obtain cluster centroids which could be used as filters for feature extraction. In the second phase, we apply conventional k-means to the representations extracted by the centroids and then project cluster labels to the target images. We evaluated our methods on pathology images of lung cancer specimen. Our experiments showed that the proposed method outperforms traditional k-means segmentation and the multithreshold Otsu method both quantitatively and qualitatively with an improved normalized mutual information (NMI) score of 0.626 compared to 0.168 and 0.167, respectively. Furthermore, we found that the centroids can be applied to the segmentation of other slices from the same sample.

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arXiv2026

Dataset-Aware Cold-Start Active Learning for Annotation-Efficient 3D Medical Image Segmentation

Deep learning for 3D medical image segmentation requires extensive manual annotations, a major bottleneck in volumetric medical imaging. Active learning aims to reduce this burden by selecting informative samples for annotation, but most methods assume that an initial labeled set is already available. This leaves the cold-start problem largely unresolved: how to select the first volumes from a fully unlabeled pool before any task-specific model is trained. We propose CSCS, a Curriculum-Stratified Cold-Start framework that adapts initial sample selection to the structure of the unlabeled dataset. CSCS combines two self-supervised, label-free signals: local typicality, measuring representativeness in the embedding space, and reconstruction-based uncertainty, used as a proxy for sample difficulty. These signals are combined through a weighted geometric score, where the weighting is determined by a closed-form pacing rule based on the effective annotation budget and the Difficulty-Coverage Ratio, a pool-level statistic measuring the alignment between difficulty and representativeness. We evaluate CSCS on four 3D medical image segmentation benchmarks: BraTS, FeTA, Spleen, and an in-house fetal MRI dataset. Using nnU-Net as downstream segmentation model, CSCS shows consistently competitive performance across datasets and annotation budgets, with the strongest gains in low-to-mid annotation regimes. These results suggest that dataset-aware cold-start initialization can improve the robustness of active learning for 3D medical image segmentation by adapting sample selection to the geometry of the unlabeled pool.

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arXiv2025

KAN-Mamba FusionNet: Redefining Medical Image Segmentation with Non-Linear Modeling

Medical image segmentation is essential for applications like robotic surgeries, disease diagnosis, and treatment planning. Recently, various deep-learning models have been proposed to enhance medical image segmentation. One promising approach utilizes Kolmogorov-Arnold Networks (KANs), which better capture non-linearity in input data. However, they are unable to effectively capture long-range dependencies, which are required to accurately segment complex medical images and, by that, improve diagnostic accuracy in clinical settings. Neural networks such as Mamba can handle long-range dependencies. However, they have a limited ability to accurately capture non-linearities in the images as compared to KANs. Thus, we propose a novel architecture, the KAN-Mamba FusionNet, which improves segmentation accuracy by effectively capturing the non-linearities from input and handling long-range dependencies with the newly proposed KAMBA block. We evaluated the proposed KAN-Mamba FusionNet on three distinct medical image segmentation datasets: BUSI, Kvasir-Seg, and GlaS - and found it consistently outperforms state-of-the-art methods in IoU and F1 scores. Further, we examined the effects of various components and assessed their contributions to the overall model performance via ablation studies. The findings highlight the effectiveness of this methodology for reliable medical image segmentation, providing a unique approach to address intricate visual data issues in healthcare.

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arXiv2025

Self-Attention Diffusion Models for Zero-Shot Biomedical Image Segmentation: Unlocking New Frontiers in Medical Imaging

Producing high-quality segmentation masks for medical images is a fundamental challenge in biomedical image analysis. Recent research has explored large-scale supervised training to enable segmentation across various medical imaging modalities and unsupervised training to facilitate segmentation without dense annotations. However, constructing a model capable of segmenting diverse medical images in a zero-shot manner without any annotations remains a significant hurdle. This paper introduces the Attention Diffusion Zero-shot Unsupervised System (ADZUS), a novel approach that leverages self-attention diffusion models for zero-shot biomedical image segmentation. ADZUS harnesses the intrinsic capabilities of pre-trained diffusion models, utilizing their generative and discriminative potentials to segment medical images without requiring annotated training data or prior domain-specific knowledge. The ADZUS architecture is detailed, with its integration of self-attention mechanisms that facilitate context-aware and detail-sensitive segmentations being highlighted. Experimental results across various medical imaging datasets, including skin lesion segmentation, chest X-ray infection segmentation, and white blood cell segmentation, reveal that ADZUS achieves state-of-the-art performance. Notably, ADZUS reached Dice scores ranging from 88.7\% to 92.9\% and IoU scores from 66.3\% to 93.3\% across different segmentation tasks, demonstrating significant improvements in handling novel, unseen medical imagery. It is noteworthy that while ADZUS demonstrates high effectiveness, it demands substantial computational resources and extended processing times. The model's efficacy in zero-shot settings underscores its potential to reduce reliance on costly annotations and seamlessly adapt to new medical imaging tasks, thereby expanding the diagnostic capabilities of AI-driven medical imaging technologies.

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arXiv2026

Understanding From Human Perspective: A Multi-agent System for Interactive Egocentric Medical Image Segmentation

Interactive egocentric medical image segmentation (IEMIS) plays an important role in smart-glasses-assisted medical image review, segmenting the medical targets a clinician refers to from their egocentric view. Once it succeeds, the object-level visual evidence it provides strengthens the review and underpins fine-grained analysis and clinical decision-making. However, the instruction and the video both come from the user's egocentric perspective, which poses two challenges. (1) Semantic ambiguity leaves the model unable to confirm the user-intended target. (2) Visual variability makes the segmentation jump from frame to frame. In this paper, we propose EgoMed-Agent, a multi-agent system that understands the target from the human perspective through two workflows. (1) The \textit{Target Confirmation Workflow} grounds the instruction against candidate targets with a reliability score, confirming the target when the grounding is reliable and asking the user to clarify when it is not, thereby confirming the segmentation target. (2) The \textit{Localization-Guided Propagation Workflow} couples mask propagation with per-frame target localization, using the localized target to correct the propagated mask whenever the two diverge, so the segmentation stays on the target across the egocentric video. Extensive experiments show that EgoMed-Agent reaches 71.34\% average Dice, far above the best text-prompted baseline (11.70\%). Our code is available at \href{https://github.com/wdyyyyyy/EgoMed-Agent}{our project page}.

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arXiv2010

SAR Image Segmentation using Vector Quantization Technique on Entropy Images

The development and application of various remote sensing platforms result in the production of huge amounts of satellite image data. Therefore, there is an increasing need for effective querying and browsing in these image databases. In order to take advantage and make good use of satellite images data, we must be able to extract meaningful information from the imagery. Hence we proposed a new algorithm for SAR image segmentation. In this paper we propose segmentation using vector quantization technique on entropy image. Initially, we obtain entropy image and in second step we use Kekre's Fast Codebook Generation (KFCG) algorithm for segmentation of the entropy image. Thereafter, a codebook of size 128 was generated for the Entropy image. These code vectors were further clustered in 8 clusters using same KFCG algorithm and converted into 8 images. These 8 images were displayed as a result. This approach does not lead to over segmentation or under segmentation. We compared these results with well known Gray Level Co-occurrence Matrix. The proposed algorithm gives better segmentation with less complexity.

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arXiv2024

Patch-Based Deep Unsupervised Image Segmentation using Graph Cuts

Unsupervised image segmentation aims at grouping different semantic patterns in an image without the use of human annotation. Similarly, image clustering searches for groupings of images based on their semantic content without supervision. Classically, both problems have captivated researchers as they drew from sound mathematical concepts to produce concrete applications. With the emergence of deep learning, the scientific community turned its attention to complex neural network-based solvers that achieved impressive results in those domains but rarely leveraged the advances made by classical methods. In this work, we propose a patch-based unsupervised image segmentation strategy that bridges advances in unsupervised feature extraction from deep clustering methods with the algorithmic help of classical graph-based methods. We show that a simple convolutional neural network, trained to classify image patches and iteratively regularized using graph cuts, naturally leads to a state-of-the-art fully-convolutional unsupervised pixel-level segmenter. Furthermore, we demonstrate that this is the ideal setting for leveraging the patch-level pairwise features generated by vision transformer models. Our results on real image data demonstrate the effectiveness of our proposed methodology.

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arXiv2021

Spatially Dependent U-Nets: Highly Accurate Architectures for Medical Imaging Segmentation

In clinical practice, regions of interest in medical imaging often need to be identified through a process of precise image segmentation. The quality of this image segmentation step critically affects the subsequent clinical assessment of the patient status. To enable high accuracy, automatic image segmentation, we introduce a novel deep neural network architecture that exploits the inherent spatial coherence of anatomical structures and is well equipped to capture long-range spatial dependencies in the segmented pixel/voxel space. In contrast to the state-of-the-art solutions based on convolutional layers, our approach leverages on recently introduced spatial dependency layers that have an unbounded receptive field and explicitly model the inductive bias of spatial coherence. Our method performs favourably to commonly used U-Net and U-Net++ architectures as demonstrated by improved Dice and Jaccardscore in three different medical segmentation tasks: nuclei segmentation in microscopy images, polyp segmentation in colonoscopy videos, and liver segmentation in abdominal CT scans.

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arXiv2019

Consistent estimation of the max-flow problem: Towards unsupervised image segmentation

Advances in the image-based diagnostics of complex biological and manufacturing processes have brought unsupervised image segmentation to the forefront of enabling automated, on the fly decision making. However, most existing unsupervised segmentation approaches are either computationally complex or require manual parameter selection (e.g., flow capacities in max-flow/min-cut segmentation). In this work, we present a fully unsupervised segmentation approach using a continuous max-flow formulation over the image domain while optimally estimating the flow parameters from the image characteristics. More specifically, we show that the maximum a posteriori estimate of the image labels can be formulated as a continuous max-flow problem given the flow capacities are known. The flow capacities are then iteratively obtained by employing a novel Markov random field prior over the image domain. We present theoretical results to establish the posterior consistency of the flow capacities. We compare the performance of our approach on two real-world case studies including brain tumor image segmentation and defect identification in additively manufactured components using electron microscopic images. Comparative results with several state-of-the-art supervised as well as unsupervised methods suggest that the present method performs statistically similar to the supervised methods, but results in more than 90% improvement in the Dice score when compared to the state-of-the-art unsupervised methods.

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