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arXiv2026

MAAPO:an innovative membrane algorithm based on artificial protozoa optimizer for multilevel threshold image segmentation

This paper proposes a novel membrane algorithm based on artificial protozoa optimizer (MAAPO) for global optimization problems. The artificial protozoa optimizer (APO) is adopted as the base meta-heuristic algorithm due to its novelty and competitive performance. MAAPO integrates two key innovations:(1) a membrane computing (MC) framework that introduces a parallel distributed paradigm to improve population diversity and search dynamics, and (2) an enhanced autotrophic model within APO that uses a roulette-based fitness-distance balance (RFDB) mechanism for adaptive reference point selection. These strategies collectively enhance the algorithm's exploration-exploitation balance and global search capabilities. To validate its performance, MAAPO is tested against 12 advanced algorithms on the CEC2017 test suite, and further applied to the multilevel thresholding image segmentation problem using Otsu and Kapur entropy as objective functions. The quality of segmented images is assessed using peak signal-to-noise ratio (PSNR), structural similarity index (SSIM), and feature similarity index (FSIM) metrics. Experimental results demonstrate that MAAPO outperforms its counterparts, delivering superior segmentation quality. This research on MAAPO contributes an effective enhancement strategy to meta-heuristic algorithms and introduces a novel, highly applicable approach for complex image segmentation tasks.

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arXiv2023

Pick the Best Pre-trained Model: Towards Transferability Estimation for Medical Image Segmentation

Transfer learning is a critical technique in training deep neural networks for the challenging medical image segmentation task that requires enormous resources. With the abundance of medical image data, many research institutions release models trained on various datasets that can form a huge pool of candidate source models to choose from. Hence, it's vital to estimate the source models' transferability (i.e., the ability to generalize across different downstream tasks) for proper and efficient model reuse. To make up for its deficiency when applying transfer learning to medical image segmentation, in this paper, we therefore propose a new Transferability Estimation (TE) method. We first analyze the drawbacks of using the existing TE algorithms for medical image segmentation and then design a source-free TE framework that considers both class consistency and feature variety for better estimation. Extensive experiments show that our method surpasses all current algorithms for transferability estimation in medical image segmentation. Code is available at https://github.com/EndoluminalSurgicalVision-IMR/CCFV

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arXiv2022

Synthetic Data for Semantic Image Segmentation of Imagery of Unmanned Spacecraft

Images of spacecraft photographed from other spacecraft operating in outer space are difficult to come by, especially at a scale typically required for deep learning tasks. Semantic image segmentation, object detection and localization, and pose estimation are well researched areas with powerful results for many applications, and would be very useful in autonomous spacecraft operation and rendezvous. However, recent studies show that these strong results in broad and common domains may generalize poorly even to specific industrial applications on earth. To address this, we propose a method for generating synthetic image data that are labelled for semantic segmentation, generalizable to other tasks, and provide a prototype synthetic image dataset consisting of 2D monocular images of unmanned spacecraft, in order to enable further research in the area of autonomous spacecraft rendezvous. We also present a strong benchmark result (Sørensen-Dice coefficient 0.8723) on these synthetic data, suggesting that it is feasible to train well-performing image segmentation models for this task, especially if the target spacecraft and its configuration are known.

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arXiv2023

Multiscale Progressive Text Prompt Network for Medical Image Segmentation

The accurate segmentation of medical images is a crucial step in obtaining reliable morphological statistics. However, training a deep neural network for this task requires a large amount of labeled data to ensure high-accuracy results. To address this issue, we propose using progressive text prompts as prior knowledge to guide the segmentation process. Our model consists of two stages. In the first stage, we perform contrastive learning on natural images to pretrain a powerful prior prompt encoder (PPE). This PPE leverages text prior prompts to generate multimodality features. In the second stage, medical image and text prior prompts are sent into the PPE inherited from the first stage to achieve the downstream medical image segmentation task. A multiscale feature fusion block (MSFF) combines the features from the PPE to produce multiscale multimodality features. These two progressive features not only bridge the semantic gap but also improve prediction accuracy. Finally, an UpAttention block refines the predicted results by merging the image and text features. This design provides a simple and accurate way to leverage multiscale progressive text prior prompts for medical image segmentation. Compared with using only images, our model achieves high-quality results with low data annotation costs. Moreover, our model not only has excellent reliability and validity on medical images but also performs well on natural images. The experimental results on different image datasets demonstrate that our model is effective and robust for image segmentation.

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arXiv2023

Medical Image Segmentation with Belief Function Theory and Deep Learning

Deep learning has shown promising contributions in medical image segmentation with powerful learning and feature representation abilities. However, it has limitations for reasoning with and combining imperfect (imprecise, uncertain, and partial) information. In this thesis, we study medical image segmentation approaches with belief function theory and deep learning, specifically focusing on information modeling and fusion based on uncertain evidence. First, we review existing belief function theory-based medical image segmentation methods and discuss their advantages and challenges. Second, we present a semi-supervised medical image segmentation framework to decrease the uncertainty caused by the lack of annotations with evidential segmentation and evidence fusion. Third, we compare two evidential classifiers, evidential neural network and radial basis function network, and show the effectiveness of belief function theory in uncertainty quantification; we use the two evidential classifiers with deep neural networks to construct deep evidential models for lymphoma segmentation. Fourth, we present a multimodal medical image fusion framework taking into account the reliability of each MR image source when performing different segmentation tasks using mass functions and contextual discounting.

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arXiv2021

Medical Image Segmentation Using Deep Learning: A Survey

Deep learning has been widely used for medical image segmentation and a large number of papers has been presented recording the success of deep learning in the field. In this paper, we present a comprehensive thematic survey on medical image segmentation using deep learning techniques. This paper makes two original contributions. Firstly, compared to traditional surveys that directly divide literatures of deep learning on medical image segmentation into many groups and introduce literatures in detail for each group, we classify currently popular literatures according to a multi-level structure from coarse to fine. Secondly, this paper focuses on supervised and weakly supervised learning approaches, without including unsupervised approaches since they have been introduced in many old surveys and they are not popular currently. For supervised learning approaches, we analyze literatures in three aspects: the selection of backbone networks, the design of network blocks, and the improvement of loss functions. For weakly supervised learning approaches, we investigate literature according to data augmentation, transfer learning, and interactive segmentation, separately. Compared to existing surveys, this survey classifies the literatures very differently from before and is more convenient for readers to understand the relevant rationale and will guide them to think of appropriate improvements in medical image segmentation based on deep learning approaches.

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arXiv2026

RobustMedSAM: Degradation-Resilient Medical Image Segmentation via Robust Foundation Model Adaptation

Medical image segmentation models built on Segment Anything Model (SAM) achieve strong performance on clean benchmarks, yet their reliability often degrades under realistic image corruptions such as noise, blur, motion artifacts, and modality-specific distortions. Existing approaches address either medical-domain adaptation or corruption robustness, but not both jointly. In SAM, we find that these capabilities are concentrated in complementary modules: the image encoder preserves medical priors, while the mask decoder governs corruption robustness. Motivated by this observation, we propose RobustMedSAM, which adopts module-wise checkpoint fusion by initializing the image encoder from MedSAM and the mask decoder from RobustSAM under a shared ViT-B architecture. We then fine-tune only the mask decoder on 35 medical datasets from MedSegBench, spanning six imaging modalities and 12 corruption types, while freezing the remaining components to preserve pretrained medical representations. We additionally investigate an SVD-based parameter-efficient variant for limited encoder adaptation. Experiments on both in-distribution and out-of-distribution benchmarks show that RobustMedSAM improves degraded-image Dice from 0.613 to 0.719 (+0.106) over SAM, demonstrating that structured fusion of complementary pretrained models is an effective and practical approach for robust medical image segmentation.

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arXiv2018

Improved Image Segmentation via Cost Minimization of Multiple Hypotheses

Image segmentation is an important component of many image understanding systems. It aims to group pixels in a spatially and perceptually coherent manner. Typically, these algorithms have a collection of parameters that control the degree of over-segmentation produced. It still remains a challenge to properly select such parameters for human-like perceptual grouping. In this work, we exploit the diversity of segments produced by different choices of parameters. We scan the segmentation parameter space and generate a collection of image segmentation hypotheses (from highly over-segmented to under-segmented). These are fed into a cost minimization framework that produces the final segmentation by selecting segments that: (1) better describe the natural contours of the image, and (2) are more stable and persistent among all the segmentation hypotheses. We compare our algorithm's performance with state-of-the-art algorithms, showing that we can achieve improved results. We also show that our framework is robust to the choice of segmentation kernel that produces the initial set of hypotheses.

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arXiv2023

A Survey on Label-efficient Deep Image Segmentation: Bridging the Gap between Weak Supervision and Dense Prediction

The rapid development of deep learning has made a great progress in image segmentation, one of the fundamental tasks of computer vision. However, the current segmentation algorithms mostly rely on the availability of pixel-level annotations, which are often expensive, tedious, and laborious. To alleviate this burden, the past years have witnessed an increasing attention in building label-efficient, deep-learning-based image segmentation algorithms. This paper offers a comprehensive review on label-efficient image segmentation methods. To this end, we first develop a taxonomy to organize these methods according to the supervision provided by different types of weak labels (including no supervision, inexact supervision, incomplete supervision and inaccurate supervision) and supplemented by the types of segmentation problems (including semantic segmentation, instance segmentation and panoptic segmentation). Next, we summarize the existing label-efficient image segmentation methods from a unified perspective that discusses an important question: how to bridge the gap between weak supervision and dense prediction -- the current methods are mostly based on heuristic priors, such as cross-pixel similarity, cross-label constraint, cross-view consistency, and cross-image relation. Finally, we share our opinions about the future research directions for label-efficient deep image segmentation.

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arXiv2025

Data Efficiency and Transfer Robustness in Biomedical Image Segmentation: A Study of Redundancy and Forgetting with Cellpose

Generalist biomedical image segmentation models such as Cellpose are increasingly applied across diverse imaging modalities and cell types. However, two critical challenges remain underexplored: (1) the extent of training data redundancy and (2) the impact of cross domain transfer on model retention. In this study, we conduct a systematic empirical analysis of these challenges using Cellpose as a case study. First, to assess data redundancy, we propose a simple dataset quantization (DQ) strategy for constructing compact yet diverse training subsets. Experiments on the Cyto dataset show that image segmentation performance saturates with only 10% of the data, revealing substantial redundancy and potential for training with minimal annotations. Latent space analysis using MAE embeddings and t-SNE confirms that DQ selected patches capture greater feature diversity than random sampling. Second, to examine catastrophic forgetting, we perform cross domain finetuning experiments and observe significant degradation in source domain performance, particularly when adapting from generalist to specialist domains. We demonstrate that selective DQ based replay reintroducing just 5-10% of the source data effectively restores source performance, while full replay can hinder target adaptation. Additionally, we find that training domain sequencing improves generalization and reduces forgetting in multi stage transfer. Our findings highlight the importance of data centric design in biomedical image segmentation and suggest that efficient training requires not only compact subsets but also retention aware learning strategies and informed domain ordering. The code is available at https://github.com/MMV-Lab/biomedseg-efficiency.

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arXiv2026

RADA: Region-Aware Dual-encoder Auxiliary learning for Barely-supervised Medical Image Segmentation

Deep learning has greatly advanced medical image segmentation, but its success relies heavily on fully supervised learning, which requires dense annotations that are costly and time-consuming for 3D volumetric scans. Barely-supervised learning reduces annotation burden by using only a few labeled slices per volume. Existing methods typically propagate sparse annotations to unlabeled slices through geometric continuity to generate pseudo-labels, but this strategy lacks semantic understanding, often resulting in low-quality pseudo-labels. Furthermore, medical image segmentation is inherently a pixel-level visual understanding task, where accuracy fundamentally depends on the quality of local, fine-grained visual features. Inspired by this, we propose RADA, a novel Region-Aware Dual-encoder Auxiliary learning pipeline which introduces a dual-encoder framework pre-trained on Alpha-CLIP to extract fine-grained, region-specific visual features from the original images and limited annotations. The framework combines image-level fine-grained visual features with text-level semantic guidance, providing region-aware semantic supervision that bridges image-level semantics and pixel-level segmentation. Integrated into a triple-view training framework, RADA achieves SOTA performance under extremely sparse annotation settings on LA2018, KiTS19 and LiTS, demonstrating robust generalization across diverse datasets.

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arXiv2019

Automated Quality Control in Image Segmentation: Application to the UK Biobank Cardiac MR Imaging Study

Background: The trend towards large-scale studies including population imaging poses new challenges in terms of quality control (QC). This is a particular issue when automatic processing tools, e.g. image segmentation methods, are employed to derive quantitative measures or biomarkers for later analyses. Manual inspection and visual QC of each segmentation isn't feasible at large scale. However, it's important to be able to automatically detect when a segmentation method fails so as to avoid inclusion of wrong measurements into subsequent analyses which could lead to incorrect conclusions. Methods: To overcome this challenge, we explore an approach for predicting segmentation quality based on Reverse Classification Accuracy, which enables us to discriminate between successful and failed segmentations on a per-cases basis. We validate this approach on a new, large-scale manually-annotated set of 4,800 cardiac magnetic resonance scans. We then apply our method to a large cohort of 7,250 cardiac MRI on which we have performed manual QC. Results: We report results used for predicting segmentation quality metrics including Dice Similarity Coefficient (DSC) and surface-distance measures. As initial validation, we present data for 400 scans demonstrating 99% accuracy for classifying low and high quality segmentations using predicted DSC scores. As further validation we show high correlation between real and predicted scores and 95% classification accuracy on 4,800 scans for which manual segmentations were available. We mimic real-world application of the method on 7,250 cardiac MRI where we show good agreement between predicted quality metrics and manual visual QC scores. Conclusions: We show that RCA has the potential for accurate and fully automatic segmentation QC on a per-case basis in the context of large-scale population imaging as in the UK Biobank Imaging Study.

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arXiv2024

Deep Self-Cleansing for Medical Image Segmentation with Noisy Labels

Medical image segmentation is crucial in the field of medical imaging, aiding in disease diagnosis and surgical planning. Most established segmentation methods rely on supervised deep learning, in which clean and precise labels are essential for supervision and significantly impact the performance of models. However, manually delineated labels often contain noise, such as missing labels and inaccurate boundary delineation, which can hinder networks from correctly modeling target characteristics. In this paper, we propose a deep self-cleansing segmentation framework that can preserve clean labels while cleansing noisy ones in the training phase. To achieve this, we devise a gaussian mixture model-based label filtering module that distinguishes noisy labels from clean labels. Additionally, we develop a label cleansing module to generate pseudo low-noise labels for identified noisy samples. The preserved clean labels and pseudo-labels are then used jointly to supervise the network. Validated on a clinical liver tumor dataset and a public cardiac diagnosis dataset, our method can effectively suppress the interference from noisy labels and achieve prominent segmentation performance.

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arXiv2016

Combining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation

Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved state-of-the-art segmentation perfor- mance. To exploit the 3D contexts using neural networks, known DL segmentation methods, including 3D convolution, 2D convolution on planes orthogonal to 2D image slices, and LSTM in multiple directions, all suffer incompatibility with the highly anisotropic dimensions in common 3D biomedical images. In this paper, we propose a new DL framework for 3D image segmentation, based on a com- bination of a fully convolutional network (FCN) and a recurrent neural network (RNN), which are responsible for exploiting the intra-slice and inter-slice contexts, respectively. To our best knowledge, this is the first DL framework for 3D image segmentation that explicitly leverages 3D image anisotropism. Evaluating using a dataset from the ISBI Neuronal Structure Segmentation Challenge and in-house image stacks for 3D fungus segmentation, our approach achieves promising results comparing to the known DL-based 3D segmentation approaches.

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arXiv2024

SliceMamba with Neural Architecture Search for Medical Image Segmentation

Despite the progress made in Mamba-based medical image segmentation models, existing methods utilizing unidirectional or multi-directional feature scanning mechanisms struggle to effectively capture dependencies between neighboring positions, limiting the discriminant representation learning of local features. These local features are crucial for medical image segmentation as they provide critical structural information about lesions and organs. To address this limitation, we propose SliceMamba, a simple and effective locally sensitive Mamba-based medical image segmentation model. SliceMamba includes an efficient Bidirectional Slice Scan module (BSS), which performs bidirectional feature slicing and employs varied scanning mechanisms for sliced features with distinct shapes. This design ensures that spatially adjacent features remain close in the scanning sequence, thereby improving segmentation performance. Additionally, to fit the varying sizes and shapes of lesions and organs, we further introduce an Adaptive Slice Search method to automatically determine the optimal feature slice method based on the characteristics of the target data. Extensive experiments on two skin lesion datasets (ISIC2017 and ISIC2018), two polyp segmentation (Kvasir and ClinicDB) datasets, and one multi-organ segmentation dataset (Synapse) validate the effectiveness of our method.

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arXiv2023

Selecting the Best Optimizers for Deep Learning based Medical Image Segmentation

The goal of this work is to identify the best optimizers for deep learning in the context of cardiac image segmentation and to provide guidance on how to design segmentation networks with effective optimization strategies. Adaptive learning helps with fast convergence by starting with a larger learning rate (LR) and gradually decreasing it. Momentum optimizers are particularly effective at quickly optimizing neural networks within the accelerated schemes category. By revealing the potential interplay between these two types of algorithms (LR and momentum optimizers or momentum rate (MR) in short), in this article, we explore the two variants of SGD algorithms in a single setting. We suggest using cyclic learning as the base optimizer and integrating optimal values of learning rate and momentum rate. We investigated the relationship of LR and MR under an important problem of medical image segmentation of cardiac structures from MRI and CT scans. We conducted experiments using the cardiac imaging dataset from the ACDC challenge of MICCAI 2017, and four different architectures shown to be successful for cardiac image segmentation problems. Our comprehensive evaluations demonstrated that the proposed optimizer achieved better results (over a 2\% improvement in the dice metric) than other optimizers in deep learning literature with similar or lower computational cost in both single and multi-object segmentation settings. We hypothesized that combination of accelerated and adaptive optimization methods can have a drastic effect in medical image segmentation performances. To this end, we proposed a new cyclic optimization method (\textit{CLMR}) to address the efficiency and accuracy problems in deep learning based medical image segmentation. The proposed strategy yielded better generalization in comparison to adaptive optimizers.

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arXiv2022

Label Refinement Network from Synthetic Error Augmentation for Medical Image Segmentation

Deep convolutional neural networks for image segmentation do not learn the label structure explicitly and may produce segmentations with an incorrect structure, e.g., with disconnected cylindrical structures in the segmentation of tree-like structures such as airways or blood vessels. In this paper, we propose a novel label refinement method to correct such errors from an initial segmentation, implicitly incorporating information about label structure. This method features two novel parts: 1) a model that generates synthetic structural errors, and 2) a label appearance simulation network that produces synthetic segmentations (with errors) that are similar in appearance to the real initial segmentations. Using these synthetic segmentations and the original images, the label refinement network is trained to correct errors and improve the initial segmentations. The proposed method is validated on two segmentation tasks: airway segmentation from chest computed tomography (CT) scans and brain vessel segmentation from 3D CT angiography (CTA) images of the brain. In both applications, our method significantly outperformed a standard 3D U-Net and other previous refinement approaches. Improvements are even larger when additional unlabeled data is used for model training. In an ablation study, we demonstrate the value of the different components of the proposed method.

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arXiv2024

RevSAM2: Prompt SAM2 for Medical Image Segmentation via Reverse-Propagation without Fine-tuning

The Segment Anything Model 2 (SAM2) has recently demonstrated exceptional performance in zero-shot prompt segmentation for natural images and videos. However, when the propagation mechanism of SAM2 is applied to medical images, it often results in spatial inconsistencies, leading to significantly different segmentation outcomes for very similar images. In this paper, we introduce RevSAM2, a simple yet effective self-correction framework that enables SAM2 to achieve superior performance in unseen 3D medical image segmentation tasks without the need for fine-tuning. Specifically, to segment a 3D query volume using a limited number of support image-label pairs that define a new segmentation task, we propose reverse propagation strategy as a query information selection mechanism. Instead of simply maintaining a first-in-first-out (FIFO) queue of memories to predict query slices sequentially, reverse propagation selects high-quality query information by leveraging support images to evaluate the quality of each predicted query slice mask. The selected high-quality masks are then used as prompts to propagate across the entire query volume, thereby enhancing generalization to unseen tasks. Notably, we are the first to explore the potential of SAM2 in label-efficient medical image segmentation without fine-tuning. Compared to fine-tuning on large labeled datasets, the label-efficient scenario provides a cost-effective alternative for medical segmentation tasks, particularly for rare diseases or when dealing with unseen classes. Experiments on four public datasets demonstrate the superiority of RevSAM2 in scenarios with limited labels, surpassing state-of-the-arts by 12.18% in Dice. The code will be released.

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