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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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arXiv2023

Interpretable Small Training Set Image Segmentation Network Originated from Multi-Grid Variational Model

The main objective of image segmentation is to divide an image into homogeneous regions for further analysis. This is a significant and crucial task in many applications such as medical imaging. Deep learning (DL) methods have been proposed and widely used for image segmentation. However, these methods usually require a large amount of manually segmented data as training data and suffer from poor interpretability (known as the black box problem). The classical Mumford-Shah (MS) model is effective for segmentation and provides a piece-wise smooth approximation of the original image. In this paper, we replace the hand-crafted regularity term in the MS model with a data adaptive generalized learnable regularity term and use a multi-grid framework to unroll the MS model and obtain a variational model-based segmentation network with better generalizability and interpretability. This approach allows for the incorporation of learnable prior information into the network structure design. Moreover, the multi-grid framework enables multi-scale feature extraction and offers a mathematical explanation for the effectiveness of the U-shaped network structure in producing good image segmentation results. Due to the proposed network originates from a variational model, it can also handle small training sizes. Our experiments on the REFUGE dataset, the White Blood Cell image dataset, and 3D thigh muscle magnetic resonance (MR) images demonstrate that even with smaller training datasets, our method yields better segmentation results compared to related state of the art segmentation methods.

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arXiv2024

KA$^2$ER: Knowledge Adaptive Amalgamation of ExpeRts for Medical Images Segmentation

Recently, many foundation models for medical image analysis such as MedSAM, SwinUNETR have been released and proven to be useful in multiple tasks. However, considering the inherent heterogeneity and inhomogeneity of real-world medical data, directly applying these models to specific medical image segmentation tasks often leads to negative domain shift effects, which can severely weaken the model's segmentation capabilities. To this end, we propose an adaptive amalgamation knowledge framework that aims to train a versatile foundation model to handle the joint goals of multiple expert models, each specialized for a distinct task. Specifically, we first train an nnUNet-based expert model for each task, and reuse the pre-trained SwinUNTER as the target foundation model. Then, the input data for all challenging tasks are encoded in the foundation model and the expert models, respectively, and their backbone features are jointly projected into the adaptive amalgamation layer. Within the hidden layer, the hierarchical attention mechanisms are designed to achieve adaptive merging of the target model to the hidden layer feature knowledge of all experts, which significantly reduces the domain shift arising from the inter-task differences. Finally, the gold amalgamated features and the prompt features are fed into the mask decoder to obtain the segmentation results. Extensive experiments conducted in these challenging tasks demonstrate the effectiveness and adaptability of our foundation model for real-world medical image segmentation.

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arXiv2023

Explainable Semantic Medical Image Segmentation with Style

Semantic medical image segmentation using deep learning has recently achieved high accuracy, making it appealing to clinical problems such as radiation therapy. However, the lack of high-quality semantically labelled data remains a challenge leading to model brittleness to small shifts to input data. Most works require extra data for semi-supervised learning and lack the interpretability of the boundaries of the training data distribution during training, which is essential for model deployment in clinical practice. We propose a fully supervised generative framework that can achieve generalisable segmentation with only limited labelled data by simultaneously constructing an explorable manifold during training. The proposed approach creates medical image style paired with a segmentation task driven discriminator incorporating end-to-end adversarial training. The discriminator is generalised to small domain shifts as much as permissible by the training data, and the generator automatically diversifies the training samples using a manifold of input features learnt during segmentation. All the while, the discriminator guides the manifold learning by supervising the semantic content and fine-grained features separately during the image diversification. After training, visualisation of the learnt manifold from the generator is available to interpret the model limits. Experiments on a fully semantic, publicly available pelvis dataset demonstrated that our method is more generalisable to shifts than other state-of-the-art methods while being more explainable using an explorable manifold.

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arXiv2025

Semi-Supervised Medical Image Segmentation via Dual Networks

Traditional supervised medical image segmentation models require large amounts of labeled data for training; however, obtaining such large-scale labeled datasets in the real world is extremely challenging. Recent semi-supervised segmentation models also suffer from noisy pseudo-label issue and limited supervision in feature space. To solve these challenges, we propose an innovative semi-supervised 3D medical image segmentation method to reduce the dependency on large, expert-labeled datasets. Furthermore, we introduce a dual-network architecture to address the limitations of existing methods in using contextual information and generating reliable pseudo-labels. In addition, a self-supervised contrastive learning strategy is used to enhance the representation of the network and reduce prediction uncertainty by distinguishing between reliable and unreliable predictions. Experiments on clinical magnetic resonance imaging demonstrate that our approach outperforms state-of-the-art techniques. Our code is available at https://github.com/AIPMLab/Semi-supervised-Segmentation.

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arXiv2026

Eye image segmentation using visual and concept prompts with Segment Anything Model 3 (SAM3)

Previous work has reported that vision foundation models show promising zero-shot performance in eye image segmentation. Here we examine whether the latest iteration of the Segment Anything Model, SAM3, offers better eye image segmentation performance than SAM2, and explore the performance of its new concept (text) prompting mode. Eye image segmentation performance was evaluated using diverse datasets encompassing both high-resolution high-quality videos from a lab environment and the TEyeD dataset consisting of challenging eye videos acquired in the wild. Results show that in most cases SAM3 with either visual or concept prompts did not perform better than SAM2, for both lab and in-the-wild datasets. Since SAM2 not only performed better but was also faster, we conclude that SAM2 remains the best option for eye image segmentation. We provide our adaptation of SAM3's codebase that allows processing videos of arbitrary duration.

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arXiv2025

NSegment : Label-specific Deformations for Remote Sensing Image Segmentation

Labeling errors in remote sensing (RS) image segmentation datasets often remain implicit and subtle due to ambiguous class boundaries, mixed pixels, shadows, complex terrain features, and subjective annotator bias. Furthermore, the scarcity of annotated RS data due to the high cost of labeling complicates training noise-robust models. While sophisticated mechanisms such as label selection or noise correction might address the issue mentioned above, they tend to increase training time and add implementation complexity. In this paper, we propose NSegment-a simple yet effective data augmentation solution to mitigate this issue. Unlike traditional methods, it applies elastic transformations only to segmentation labels, varying deformation intensity per sample in each training epoch to address annotation inconsistencies. Experimental results demonstrate that our approach improves the performance of RS image segmentation over various state-of-the-art models.

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arXiv2025

Uncertainty-aware Cross-training for Semi-supervised Medical Image Segmentation

Semi-supervised learning has gained considerable popularity in medical image segmentation tasks due to its capability to reduce reliance on expert-examined annotations. Several mean-teacher (MT) based semi-supervised methods utilize consistency regularization to effectively leverage valuable information from unlabeled data. However, these methods often heavily rely on the student model and overlook the potential impact of cognitive biases within the model. Furthermore, some methods employ co-training using pseudo-labels derived from different inputs, yet generating high-confidence pseudo-labels from perturbed inputs during training remains a significant challenge. In this paper, we propose an Uncertainty-aware Cross-training framework for semi-supervised medical image Segmentation (UC-Seg). Our UC-Seg framework incorporates two distinct subnets to effectively explore and leverage the correlation between them, thereby mitigating cognitive biases within the model. Specifically, we present a Cross-subnet Consistency Preservation (CCP) strategy to enhance feature representation capability and ensure feature consistency across the two subnets. This strategy enables each subnet to correct its own biases and learn shared semantics from both labeled and unlabeled data. Additionally, we propose an Uncertainty-aware Pseudo-label Generation (UPG) component that leverages segmentation results and corresponding uncertainty maps from both subnets to generate high-confidence pseudo-labels. We extensively evaluate the proposed UC-Seg on various medical image segmentation tasks involving different modality images, such as MRI, CT, ultrasound, colonoscopy, and so on. The results demonstrate that our method achieves superior segmentation accuracy and generalization performance compared to other state-of-the-art semi-supervised methods. Our code will be released at https://github.com/taozh2017/UCSeg.

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arXiv2024

Self-Paced Sample Selection for Barely-Supervised Medical Image Segmentation

The existing barely-supervised medical image segmentation (BSS) methods, adopting a registration-segmentation paradigm, aim to learn from data with very few annotations to mitigate the extreme label scarcity problem. However, this paradigm poses a challenge: pseudo-labels generated by image registration come with significant noise. To address this issue, we propose a self-paced sample selection framework (SPSS) for BSS. Specifically, SPSS comprises two main components: 1) self-paced uncertainty sample selection (SU) for explicitly improving the quality of pseudo labels in the image space, and 2) self-paced bidirectional feature contrastive learning (SC) for implicitly improving the quality of pseudo labels through enhancing the separability between class semantics in the feature space. Both SU and SC are trained collaboratively in a self-paced learning manner, ensuring that SPSS can learn from high-quality pseudo labels for BSS. Extensive experiments on two public medical image segmentation datasets demonstrate the effectiveness and superiority of SPSS over the state-of-the-art. Our code is release at https://github.com/SuuuJM/SPSS.

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arXiv2015

Joint Color-Spatial-Directional clustering and Region Merging (JCSD-RM) for unsupervised RGB-D image segmentation

Recent advances in depth imaging sensors provide easy access to the synchronized depth with color, called RGB-D image. In this paper, we propose an unsupervised method for indoor RGB-D image segmentation and analysis. We consider a statistical image generation model based on the color and geometry of the scene. Our method consists of a joint color-spatial-directional clustering method followed by a statistical planar region merging method. We evaluate our method on the NYU depth database and compare it with existing unsupervised RGB-D segmentation methods. Results show that, it is comparable with the state of the art methods and it needs less computation time. Moreover, it opens interesting perspectives to fuse color and geometry in an unsupervised manner.

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arXiv2022

Graph Flow: Cross-layer Graph Flow Distillation for Dual Efficient Medical Image Segmentation

With the development of deep convolutional neural networks, medical image segmentation has achieved a series of breakthroughs in recent years. However, the high-performance convolutional neural networks always mean numerous parameters and high computation costs, which will hinder the applications in clinical scenarios. Meanwhile, the scarceness of large-scale annotated medical image datasets further impedes the application of high-performance networks. To tackle these problems, we propose Graph Flow, a comprehensive knowledge distillation framework, for both network-efficiency and annotation-efficiency medical image segmentation. Specifically, our core Graph Flow Distillation transfer the essence of cross-layer variations from a well-trained cumbersome teacher network to a non-trained compact student network. In addition, an unsupervised Paraphraser Module is integrated to purify the knowledge of the teacher network, which is also beneficial for the stabilization of training procedure. Furthermore, we build a unified distillation framework by integrating the adversarial distillation and the vanilla logits distillation, which can further refine the final predictions of the compact network. With different teacher networks (conventional convolutional architecture or prevalent transformer architecture) and student networks, we conduct extensive experiments on four medical image datasets with different modalities (Gastric Cancer, Synapse, BUSI, and CVC-ClinicDB).We demonstrate the prominent ability of our method which achieves competitive performance on these datasets. Moreover, we demonstrate the effectiveness of our Graph Flow through a novel semi-supervised paradigm for dual efficient medical image segmentation. Our code will be available at Graph Flow.

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arXiv2020

Transformation Consistent Self-ensembling Model for Semi-supervised Medical Image Segmentation

Deep convolutional neural networks have achieved remarkable progress on a variety of medical image computing tasks. A common problem when applying supervised deep learning methods to medical images is the lack of labeled data, which is very expensive and time-consuming to be collected. In this paper, we present a novel semi-supervised method for medical image segmentation, where the network is optimized by the weighted combination of a common supervised loss for labeled inputs only and a regularization loss for both labeled and unlabeled data. To utilize the unlabeled data, our method encourages the consistent predictions of the network-in-training for the same input under different regularizations. Aiming for the semi-supervised segmentation problem, we enhance the effect of regularization for pixel-level predictions by introducing a transformation, including rotation and flipping, consistent scheme in our self-ensembling model. With the aim of semi-supervised segmentation tasks, we introduce a transformation consistent strategy in our self-ensembling model to enhance the regularization effect for pixel-level predictions. We have extensively validated the proposed semi-supervised method on three typical yet challenging medical image segmentation tasks: (i) skin lesion segmentation from dermoscopy images on International Skin Imaging Collaboration (ISIC) 2017 dataset, (ii) optic disc segmentation from fundus images on Retinal Fundus Glaucoma Challenge (REFUGE) dataset, and (iii) liver segmentation from volumetric CT scans on Liver Tumor Segmentation Challenge (LiTS) dataset. Compared to the state-of-the-arts, our proposed method shows superior segmentation performance on challenging 2D/3D medical images, demonstrating the effectiveness of our semi-supervised method for medical image segmentation.

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arXiv2023

Two Approaches to Supervised Image Segmentation

Though performed almost effortlessly by humans, segmenting 2D gray-scale or color images into respective regions of interest (e.g.~background, objects, or portions of objects) constitutes one of the greatest challenges in science and technology as a consequence of several effects including dimensionality reduction(3D to 2D), noise, reflections, shades, and occlusions, among many other possibilities. While a large number of interesting related approaches have been suggested along the last decades, it was mainly thanks to the recent development of deep learning that more effective and general solutions have been obtained, currently constituting the basic comparison reference for this type of operation. Also developed recently, a multiset-based methodology has been described that is capable of encouraging image segmentation performance combining spatial accuracy, stability, and robustness while requiring little computational resources (hardware and/or training and recognition time). The interesting features of the multiset neurons methodology mostly follow from the enhanced selectivity and sensitivity, as well as good robustness to data perturbations and outliers, allowed by the coincidence similarity index on which the multiset approach to supervised image segmentation is founded. After describing the deep learning and multiset neurons approaches, the present work develops comparison experiments between them which are primarily aimed at illustrating their respective main interesting features when applied to the adopted specific type of data and parameter configurations. While the deep learning approach confirmed its potential for performing image segmentation, the alternative multiset methodology allowed for enhanced accuracy while requiring little computational resources.

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arXiv2026

Skill-Evolving Grounded Reasoning for Free-Text Promptable 3D Medical Image Segmentation

Free-text promptable 3D medical image segmentation offers an intuitive and clinically flexible interaction paradigm. However, current methods are highly sensitive to linguistic variability: minor changes in phrasing can cause substantial performance degradation despite identical clinical intent. Existing approaches attempt to improve robustness through stronger vision-language fusion or larger vocabularies, yet they lack mechanisms to consistently align ambiguous free-form expressions with anatomically grounded representations. We propose Skill-Evolving grounded Reasoning (SEER), a novel framework for free-text promptable 3D medical image segmentation that explicitly bridges linguistic variability and anatomical precision through a reasoning-driven design. First, we curate the SEER-Trace dataset, which pairs raw clinical requests with image-grounded, skill-tagged reasoning traces, establishing a reproducible benchmark. Second, SEER constructs an evidence-aligned target representation via a vision-language reasoning chain that verifies clinical intent against image-derived anatomical evidence, thereby enforcing semantic consistency before voxel-level decoding. Third, we introduce SEER-Loop, a dynamic skill-evolving strategy that distills high-reward reasoning trajectories into reusable skill artifacts and progressively integrates them into subsequent inference, enabling structured self-refinement and improved robustness to diverse linguistic expressions. Extensive experiments demonstrate superior performance of SEER over state-of-the-art baselines. Under linguistic perturbations, SEER reduces performance variance by 81.94% and improves worst-case Dice by 18.60%. Project page: https://seer-medseg.github.io.

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arXiv2025

Frequency-domain Multi-modal Fusion for Language-guided Medical Image Segmentation

Automatically segmenting infected areas in radiological images is essential for diagnosing pulmonary infectious diseases. Recent studies have demonstrated that the accuracy of the medical image segmentation can be improved by incorporating clinical text reports as semantic guidance. However, the complex morphological changes of lesions and the inherent semantic gap between vision-language modalities prevent existing methods from effectively enhancing the representation of visual features and eliminating semantically irrelevant information, ultimately resulting in suboptimal segmentation performance. To address these problems, we propose a Frequency-domain Multi-modal Interaction model (FMISeg) for language-guided medical image segmentation. FMISeg is a late fusion model that establishes interaction between linguistic features and frequency-domain visual features in the decoder. Specifically, to enhance the visual representation, our method introduces a Frequency-domain Feature Bidirectional Interaction (FFBI) module to effectively fuse frequency-domain features. Furthermore, a Language-guided Frequency-domain Feature Interaction (LFFI) module is incorporated within the decoder to suppress semantically irrelevant visual features under the guidance of linguistic information. Experiments on QaTa-COV19 and MosMedData+ demonstrated that our method outperforms the state-of-the-art methods qualitatively and quantitatively.

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