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arXiv2020

Y-net: Biomedical Image Segmentation and Clustering

We propose a deep clustering architecture alongside image segmentation for medical image analysis. The main idea is based on unsupervised learning to cluster images on severity of the disease in the subject's sample, and this image is then segmented to highlight and outline regions of interest. We start with training an autoencoder on the images for segmentation. The encoder part from the autoencoder branches out to a clustering node and segmentation node. Deep clustering using Kmeans clustering is performed at the clustering branch and a lightweight model is used for segmentation. Each of the branches use extracted features from the autoencoder. We demonstrate our results on ISIC 2018 Skin Lesion Analysis Towards Melanoma Detection and Cityscapes datasets for segmentation and clustering. The proposed architecture beats UNet and DeepLab results on the two datasets, and has less than half the number of parameters. We use the deep clustering branch for clustering images into four clusters. Our approach can be applied to work with high complexity datasets of medical imaging for analyzing survival prediction for severe diseases or customizing treatment based on how far the disease has propagated. Clustering patients can help understand how binning should be done on real valued features to reduce feature sparsity and improve accuracy on classification tasks. The proposed architecture can provide an early diagnosis and reduce human intervention on labeling as it can become quite costly as the datasets grow larger. The main idea is to propose a one shot approach to segmentation with deep clustering.

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arXiv2025

Pairwise Similarity Regularization for Semi-supervised Graph Medical Image Segmentation

With fully leveraging the value of unlabeled data, semi-supervised medical image segmentation algorithms significantly reduces the limitation of limited labeled data, achieving a significant improvement in accuracy. However, the distributional shift between labeled and unlabeled data weakens the utilization of information from the labeled data. To alleviate the problem, we propose a graph network feature alignment method based on pairwise similarity regularization (PaSR) for semi-supervised medical image segmentation. PaSR aligns the graph structure of images in different domains by maintaining consistency in the pairwise structural similarity of feature graphs between the target domain and the source domain, reducing distribution shift issues in medical images. Meanwhile, further improving the accuracy of pseudo-labels in the teacher network by aligning graph clustering information to enhance the semi-supervised efficiency of the model. The experimental part was verified on three medical image segmentation benchmark datasets, with results showing improvements over advanced methods in various metrics. On the ACDC dataset, it achieved an average improvement of more than 10.66%.

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arXiv2025

Fully Automated SAM for Single-source Domain Generalization in Medical Image Segmentation

Although SAM-based single-source domain generalization models for medical image segmentation can mitigate the impact of domain shift on the model in cross-domain scenarios, these models still face two major challenges. First, the segmentation of SAM is highly dependent on domain-specific expert-annotated prompts, which prevents SAM from achieving fully automated medical image segmentation and therefore limits its application in clinical settings. Second, providing poor prompts (such as bounding boxes that are too small or too large) to the SAM prompt encoder can mislead SAM into generating incorrect mask results. Therefore, we propose the FA-SAM, a single-source domain generalization framework for medical image segmentation that achieves fully automated SAM. FA-SAM introduces two key innovations: an Auto-prompted Generation Model (AGM) branch equipped with a Shallow Feature Uncertainty Modeling (SUFM) module, and an Image-Prompt Embedding Fusion (IPEF) module integrated into the SAM mask decoder. Specifically, AGM models the uncertainty distribution of shallow features through the SUFM module to generate bounding box prompts for the target domain, enabling fully automated segmentation with SAM. The IPEF module integrates multiscale information from SAM image embeddings and prompt embeddings to capture global and local details of the target object, enabling SAM to mitigate the impact of poor prompts. Extensive experiments on publicly available prostate and fundus vessel datasets validate the effectiveness of FA-SAM and highlight its potential to address the above challenges.

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arXiv2025

DFEN: Dual Feature Equalization Network for Medical Image Segmentation

Current methods for medical image segmentation primarily focus on extracting contextual feature information from the perspective of the whole image. While these methods have shown effective performance, none of them take into account the fact that pixels at the boundary and regions with a low number of class pixels capture more contextual feature information from other classes, leading to misclassification of pixels by unequal contextual feature information. In this paper, we propose a dual feature equalization network based on the hybrid architecture of Swin Transformer and Convolutional Neural Network, aiming to augment the pixel feature representations by image-level equalization feature information and class-level equalization feature information. Firstly, the image-level feature equalization module is designed to equalize the contextual information of pixels within the image. Secondly, we aggregate regions of the same class to equalize the pixel feature representations of the corresponding class by class-level feature equalization module. Finally, the pixel feature representations are enhanced by learning weights for image-level equalization feature information and class-level equalization feature information. In addition, Swin Transformer is utilized as both the encoder and decoder, thereby bolstering the ability of the model to capture long-range dependencies and spatial correlations. We conducted extensive experiments on Breast Ultrasound Images (BUSI), International Skin Imaging Collaboration (ISIC2017), Automated Cardiac Diagnosis Challenge (ACDC) and PH$^2$ datasets. The experimental results demonstrate that our method have achieved state-of-the-art performance. Our code is publicly available at https://github.com/JianJianYin/DFEN.

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arXiv2022

Distilling Ensemble of Explanations for Weakly-Supervised Pre-Training of Image Segmentation Models

While fine-tuning pre-trained networks has become a popular way to train image segmentation models, such backbone networks for image segmentation are frequently pre-trained using image classification source datasets, e.g., ImageNet. Though image classification datasets could provide the backbone networks with rich visual features and discriminative ability, they are incapable of fully pre-training the target model (i.e., backbone+segmentation modules) in an end-to-end manner. The segmentation modules are left to random initialization in the fine-tuning process due to the lack of segmentation labels in classification datasets. In our work, we propose a method that leverages Pseudo Semantic Segmentation Labels (PSSL), to enable the end-to-end pre-training for image segmentation models based on classification datasets. PSSL was inspired by the observation that the explanation results of classification models, obtained through explanation algorithms such as CAM, SmoothGrad and LIME, would be close to the pixel clusters of visual objects. Specifically, PSSL is obtained for each image by interpreting the classification results and aggregating an ensemble of explanations queried from multiple classifiers to lower the bias caused by single models. With PSSL for every image of ImageNet, the proposed method leverages a weighted segmentation learning procedure to pre-train the segmentation network en masse. Experiment results show that, with ImageNet accompanied by PSSL as the source dataset, the proposed end-to-end pre-training strategy successfully boosts the performance of various segmentation models, i.e., PSPNet-ResNet50, DeepLabV3-ResNet50, and OCRNet-HRNetW18, on a number of segmentation tasks, such as CamVid, VOC-A, VOC-C, ADE20K, and CityScapes, with significant improvements. The source code is availabel at https://github.com/PaddlePaddle/PaddleSeg.

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arXiv2022

ConvTransSeg: A Multi-resolution Convolution-Transformer Network for Medical Image Segmentation

Convolutional neural networks (CNNs) achieved the state-of-the-art performance in medical image segmentation due to their ability to extract highly complex feature representations. However, it is argued in recent studies that traditional CNNs lack the intelligence to capture long-term dependencies of different image regions. Following the success of applying Transformer models on natural language processing tasks, the medical image segmentation field has also witnessed growing interest in utilizing Transformers, due to their ability to capture long-range contextual information. However, unlike CNNs, Transformers lack the ability to learn local feature representations. Thus, to fully utilize the advantages of both CNNs and Transformers, we propose a hybrid encoder-decoder segmentation model (ConvTransSeg). It consists of a multi-layer CNN as the encoder for feature learning and the corresponding multi-level Transformer as the decoder for segmentation prediction. The encoder and decoder are interconnected in a multi-resolution manner. We compared our method with many other state-of-the-art hybrid CNN and Transformer segmentation models on binary and multiple class image segmentation tasks using several public medical image datasets, including skin lesion, polyp, cell and brain tissue. The experimental results show that our method achieves overall the best performance in terms of Dice coefficient and average symmetric surface distance measures with low model complexity and memory consumption. In contrast to most Transformer-based methods that we compared, our method does not require the use of pre-trained models to achieve similar or better performance. The code is freely available for research purposes on Github: (the link will be added upon acceptance).

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arXiv2025

Conformal Prediction for Image Segmentation Using Morphological Prediction Sets

Image segmentation is a challenging task influenced by multiple sources of uncertainty, such as the data labeling process or the sampling of training data. In this paper we focus on binary segmentation and address these challenges using conformal prediction, a family of model- and data-agnostic methods for uncertainty quantification that provide finite-sample theoretical guarantees and applicable to any pretrained predictor. Our approach involves computing nonconformity scores, a type of prediction residual, on held-out calibration data not used during training. We use dilation, one of the fundamental operations in mathematical morphology, to construct a margin added to the borders of predicted segmentation masks. At inference, the predicted set formed by the mask and its margin contains the ground-truth mask with high probability, at a confidence level specified by the user. The size of the margin serves as an indicator of predictive uncertainty for a given model and dataset. We work in a regime of minimal information as we do not require any feedback from the predictor: only the predicted masks are needed for computing the prediction sets. Hence, our method is applicable to any segmentation model, including those based on deep learning; we evaluate our approach on several medical imaging applications.

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arXiv2026

Beyond Euclidean Prototypes: Spectral Disentanglement and Geodesic Matching for Few-Shot Medical Image Segmentation

Few-Shot Medical Image Segmentation (FSMIS) aims to delineate novel anatomical targets from one or a few annotated support images, addressing the annotation scarcity in medical imaging. Notwithstanding recent advancements, current prototype-based methods are bottlenecked by two coupled limitations: 1) cue entanglement, where a single spatial-domain prototype is forced to summarise organ silhouette, parenchymal texture and boundary appearance simultaneously, so any support-query mismatch on one cue propagates indiscriminately to the others; and 2) topology-blind matching, where cosine similarity measures distance in the ambient Euclidean space and ignores the connectivity of the underlying feature manifold, causing fragmented activations inside low-contrast organs and leakage into neighbouring tissues. To this end, we propose Spectral-Geodesic Prototype Network (SGP-Net), built around a Spectral-Geodesic Prototype Module with two coupled components. A Spectral Prototype Bank (SPB) decomposes support and query features into low-, mid- and high-frequency bands via learnable radial Fourier filters, yielding three disentangled prototypes per class that separately encode shape, texture and boundary cues. A Geodesic Matcher (GM) then replaces cosine similarity with a differentiable heat-diffusion approximation of geodesic distance, propagating matching signals along a feature affinity graph so that on-manifold pixels accumulate consistent responses while off-manifold look-alikes are suppressed. Experiments on three public FSMIS benchmarks demonstrate that SGP-Net achieves competitive performance against recent state-of-the-art methods.

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arXiv2026

PSP: Harnessing Position and Shape Priors for Cross-Domain Few-Shot Medical Image Segmentation

Few-Shot Medical Image Segmentation (FSMIS) offers a powerful solution to data scarcity but struggles to generalize across different imaging modalities. This performance collapse stems primarily from the drastic texture discrepancies between domains, which mislead models trained on source-specific intensity distributions. While existing methods attempt to align frequency or local texture features, they often fail to decouple semantic structure from domain-specific appearance. To address this, we identify a critical invariance: despite distinct imaging physics, the position and geometric shape of organs remain robustly consistent across modalities. Therefore, we propose a novel framework that harnesses Position and Shape Priors (PSP) for cross-domain FSMIS. Specifically, PSP first introduces a Position Coordinate Embedding (PCE) module to inject relative spatial coordinates for rapid organ localization. Subsequently, a Shape Prototype Modulation (SPM) module constructs domain-invariant structural prototypes via explicit shape priors, effectively filtering out texture noise. Furthermore, the Hybrid-Prototype Prediction (HPP) module adaptively calibrates the support prototype to the query feature distribution, mitigating feature misalignment. Extensive experiments on two public medical imaging datasets demonstrate that PSP significantly outperforms state-of-the-art methods.

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arXiv2024

Is SAM 2 Better than SAM in Medical Image Segmentation?

The Segment Anything Model (SAM) has demonstrated impressive performance in zero-shot promptable segmentation on natural images. The recently released Segment Anything Model 2 (SAM 2) claims to outperform SAM on images and extends the model's capabilities to video segmentation. Evaluating the performance of this new model in medical image segmentation, specifically in a zero-shot promptable manner, is crucial. In this work, we conducted extensive studies using multiple datasets from various imaging modalities to compare the performance of SAM and SAM 2. We employed two point-prompt strategies: (i) multiple positive prompts where one prompt is placed near the centroid of the target structure, while the remaining prompts are randomly placed within the structure, and (ii) combined positive and negative prompts where one positive prompt is placed near the centroid of the target structure, and two negative prompts are positioned outside the structure, maximizing the distance from the positive prompt and from each other. The evaluation encompassed 24 unique organ-modality combinations, including abdominal structures, cardiac structures, fetal head images, skin lesions and polyp images across 11 publicly available MRI, CT, ultrasound, dermoscopy, and endoscopy datasets. Preliminary results based on 2D images indicate that while SAM 2 may perform slightly better in a few cases, it does not generally surpass SAM for medical image segmentation. Notably, SAM 2 performs worse than SAM in lower contrast imaging modalities, such as CT and ultrasound. However, for MRI images, SAM 2 performs on par with or better than SAM. Like SAM, SAM 2 also suffers from over-segmentation issues, particularly when the boundaries of the target organ are fuzzy.

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arXiv2019

Unsupervised Medical Image Segmentation with Adversarial Networks: From Edge Diagrams to Segmentation Maps

We develop and approach to unsupervised semantic medical image segmentation that extends previous work with generative adversarial networks. We use existing edge detection methods to construct simple edge diagrams, train a generative model to convert them into synthetic medical images, and construct a dataset of synthetic images with known segmentations using variations on extracted edge diagrams. This synthetic dataset is then used to train a supervised image segmentation model. We test our approach on a clinical dataset of kidney ultrasound images and the benchmark ISIC 2018 skin lesion dataset. We show that our unsupervised approach is more accurate than previous unsupervised methods, and performs reasonably compared to supervised image segmentation models. All code and trained models are available at https://github.com/kiretd/Unsupervised-MIseg.

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arXiv2024

Prototype Correlation Matching and Class-Relation Reasoning for Few-Shot Medical Image Segmentation

Few-shot medical image segmentation has achieved great progress in improving accuracy and efficiency of medical analysis in the biomedical imaging field. However, most existing methods cannot explore inter-class relations among base and novel medical classes to reason unseen novel classes. Moreover, the same kind of medical class has large intra-class variations brought by diverse appearances, shapes and scales, thus causing ambiguous visual characterization to degrade generalization performance of these existing methods on unseen novel classes. To address the above challenges, in this paper, we propose a \underline{\textbf{P}}rototype correlation \underline{\textbf{M}}atching and \underline{\textbf{C}}lass-relation \underline{\textbf{R}}easoning (i.e., \textbf{PMCR}) model. The proposed model can effectively mitigate false pixel correlation matches caused by large intra-class variations while reasoning inter-class relations among different medical classes. Specifically, in order to address false pixel correlation match brought by large intra-class variations, we propose a prototype correlation matching module to mine representative prototypes that can characterize diverse visual information of different appearances well. We aim to explore prototype-level rather than pixel-level correlation matching between support and query features via optimal transport algorithm to tackle false matches caused by intra-class variations. Meanwhile, in order to explore inter-class relations, we design a class-relation reasoning module to segment unseen novel medical objects via reasoning inter-class relations between base and novel classes. Such inter-class relations can be well propagated to semantic encoding of local query features to improve few-shot segmentation performance. Quantitative comparisons illustrates the large performance improvement of our model over other baseline methods.

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arXiv2024

Quantum optimization algorithms for CT image segmentation from X-ray data

Computed tomography (CT) is an important imaging technique used in medical analysis of the internal structure of the human body. Previously, image segmentation methods were required after acquiring reconstructed CT images to obtain segmented CT images which made it susceptible to errors from both reconstruction and segmentation algorithms. However, this paper introduces a new approach using an advanced quantum optimization algorithm called quadratic unconstrained binary optimization (QUBO). This algorithm enables acquisition of segmented CT images from X-ray projection data with minimized discrepancies between experimentally obtained sinograms and quantized sinograms derived from quantized segmented CT images using the Radon transform. This study utilized D-Wave's hybrid solver system for verification on real-world X-ray data.

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arXiv2022

R2U++: A Multiscale Recurrent Residual U-Net with Dense Skip Connections for Medical Image Segmentation

U-Net is a widely adopted neural network in the domain of medical image segmentation. Despite its quick embracement by the medical imaging community, its performance suffers on complicated datasets. The problem can be ascribed to its simple feature extracting blocks: encoder/decoder, and the semantic gap between encoder and decoder. Variants of U-Net (such as R2U-Net) have been proposed to address the problem of simple feature extracting blocks by making the network deeper, but it does not deal with the semantic gap problem. On the other hand, another variant UNET++ deals with the semantic gap problem by introducing dense skip connections but has simple feature extraction blocks. To overcome these issues, we propose a new U-Net based medical image segmentation architecture R2U++. In the proposed architecture, the adapted changes from vanilla U-Net are: (1) the plain convolutional backbone is replaced by a deeper recurrent residual convolution block. The increased field of view with these blocks aids in extracting crucial features for segmentation which is proven by improvement in the overall performance of the network. (2) The semantic gap between encoder and decoder is reduced by dense skip pathways. These pathways accumulate features coming from multiple scales and apply concatenation accordingly. The modified architecture has embedded multi-depth models, and an ensemble of outputs taken from varying depths improves the performance on foreground objects appearing at various scales in the images. The performance of R2U++ is evaluated on four distinct medical imaging modalities: electron microscopy (EM), X-rays, fundus, and computed tomography (CT). The average gain achieved in IoU score is 1.5+-0.37% and in dice score is 0.9+-0.33% over UNET++, whereas, 4.21+-2.72 in IoU and 3.47+-1.89 in dice score over R2U-Net across different medical imaging segmentation datasets.

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arXiv2025

TCSAFormer: Efficient Vision Transformer with Token Compression and Sparse Attention for Medical Image Segmentation

In recent years, transformer-based methods have achieved remarkable progress in medical image segmentation due to their superior ability to capture long-range dependencies. However, these methods typically suffer from two major limitations. First, their computational complexity scales quadratically with the input sequences. Second, the feed-forward network (FFN) modules in vanilla Transformers typically rely on fully connected layers, which limits models' ability to capture local contextual information and multiscale features critical for precise semantic segmentation. To address these issues, we propose an efficient medical image segmentation network, named TCSAFormer. The proposed TCSAFormer adopts two key ideas. First, it incorporates a Compressed Attention (CA) module, which combines token compression and pixel-level sparse attention to dynamically focus on the most relevant key-value pairs for each query. This is achieved by pruning globally irrelevant tokens and merging redundant ones, significantly reducing computational complexity while enhancing the model's ability to capture relationships between tokens. Second, it introduces a Dual-Branch Feed-Forward Network (DBFFN) module as a replacement for the standard FFN to capture local contextual features and multiscale information, thereby strengthening the model's feature representation capability. We conduct extensive experiments on three publicly available medical image segmentation datasets: ISIC-2018, CVC-ClinicDB, and Synapse, to evaluate the segmentation performance of TCSAFormer. Experimental results demonstrate that TCSAFormer achieves superior performance compared to existing state-of-the-art (SOTA) methods, while maintaining lower computational overhead, thus achieving an optimal trade-off between efficiency and accuracy.

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arXiv2013

Hybridization of Otsu Method and Median Filter for Color Image Segmentation

In this article a novel algorithm for color image segmentation has been developed. The proposed algorithm based on combining two existing methods in such a novel way to obtain a significant method to partition the color image into significant regions. On the first phase, the traditional Otsu method for gray channel image segmentation were applied for each of the R,G, and B channels separately to determine the suitable automatic threshold for each channel. After that, the new modified channels are integrated again to formulate a new color image. The resulted image suffers from some kind of distortion. To get rid of this distortion, the second phase is arise which is the median filter to smooth the image and increase the segmented regions. This process looks very significant by the ocular eye. Experimental results were presented on a variety of test images to support the proposed algorithm.

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arXiv2022

Mixed-Block Neural Architecture Search for Medical Image Segmentation

Deep Neural Networks (DNNs) have the potential for making various clinical procedures more time-efficient by automating medical image segmentation. Due to their strong, in some cases human-level, performance, they have become the standard approach in this field. The design of the best possible medical image segmentation DNNs, however, is task-specific. Neural Architecture Search (NAS), i.e., the automation of neural network design, has been shown to have the capability to outperform manually designed networks for various tasks. However, the existing NAS methods for medical image segmentation have explored a quite limited range of types of DNN architectures that can be discovered. In this work, we propose a novel NAS search space for medical image segmentation networks. This search space combines the strength of a generalised encoder-decoder structure, well known from U-Net, with network blocks that have proven to have a strong performance in image classification tasks. The search is performed by looking for the best topology of multiple cells simultaneously with the configuration of each cell within, allowing for interactions between topology and cell-level attributes. From experiments on two publicly available datasets, we find that the networks discovered by our proposed NAS method have better performance than well-known handcrafted segmentation networks, and outperform networks found with other NAS approaches that perform only topology search, and topology-level search followed by cell-level search.

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arXiv2025

FocusSDF: Boundary-Aware Learning for Medical Image Segmentation via Signed Distance Supervision

Segmentation of medical images constitutes an essential component of medical image analysis, providing the foundation for precise diagnosis and efficient therapeutic interventions in clinical practices. Despite substantial progress, most segmentation models do not explicitly encode boundary information; as a result, making boundary preservation a persistent challenge in medical image segmentation. To address this challenge, we introduce FocusSDF, a novel loss function based on the signed distance functions (SDFs), which redirects the network to concentrate on boundary regions by adaptively assigning higher weights to pixels closer to the lesion or organ boundary, effectively making it boundary aware. To rigorously validate FocusSDF, we perform extensive evaluations against five state-of-the-art medical image segmentation models, including the foundation model MedSAM, using four distance-based loss functions across diverse datasets covering cerebral aneurysm, stroke, liver, and breast tumor segmentation tasks spanning multiple imaging modalities. The experimental results consistently demonstrate the superior performance of FocusSDF over existing distance transform based loss functions.

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