Scribble annotations significantly reduce the cost and labor required for dense labeling in large medical datasets with complex anatomical structures. However, current scribble-supervised learning methods are limited in their ability to effectively propagate sparse annotation labels to dense segmentation masks and accurately segment object boundaries. To address these issues, we propose a Progressive Collaborative Learning framework that leverages novel algorithms and the Med-SAM foundation model to enhance information quality during training. (1) We enrich ground truth scribble segmentation labels through a new algorithm, propagating scribbles to estimate object boundaries. (2) We enhance feature representation by optimizing Med-SAM-guided training through the fusion of feature embeddings from Med-SAM and our proposed Sparse Mamba network. This enriched representation also facilitates the fine-tuning of the Med-SAM decoder with enriched scribbles. (3) For inference, we introduce a Sparse Mamba network, which is highly capable of capturing local and global dependencies by replacing the traditional sequential patch processing method with a skip-sampling procedure. Experiments on the ACDC, CHAOS, and MSCMRSeg datasets validate the effectiveness of our framework, outperforming nine state-of-the-art methods. Our code is available at \href{https://github.com/QLYCode/SparseMamba-PCL}{SparseMamba-PCL.git}.
Training of machine learning models consumes large amounts of energy. Since the energy consumption becomes a major problem in the development and implementation of artificial intelligence systems there exists a need to investigate the ways to reduce use of the resources by these systems. In this work we study how application of quantum annealers could lead to reduction of energy cost in training models aiming at pixel-level segmentation of hyperspectral images. Following the results of QBM4EO team, we propose a classical machine learning model, partially trained using quantum annealer, for hyperspectral image segmentation. We show that the model trained using quantum annealer is better or at least comparable with models trained using alternative algorithms, according to the preselected, common metrics. While direct energy use comparison does not make sense at the current stage of quantum computing technology development, we believe that our work proves that quantum annealing should be considered as a tool for training at least some machine learning models.
Zero-shot Referring Image Segmentation (RIS) identifies the instance mask that best aligns with a specified referring expression without training and fine-tuning, significantly reducing the labor-intensive annotation process. Despite achieving commendable results, previous CLIP-based models have a critical drawback: the models exhibit a notable reduction in their capacity to discern relative spatial relationships of objects. This is because they generate all possible masks on an image and evaluate each masked region for similarity to the given expression, often resulting in decreased sensitivity to direct positional clues in text inputs. Moreover, most methods have weak abilities to manage relationships between primary words and their contexts, causing confusion and reduced accuracy in identifying the correct target region. To address these challenges, we propose IteRPrimE (Iterative Grad-CAM Refinement and Primary word Emphasis), which leverages a saliency heatmap through Grad-CAM from a Vision-Language Pre-trained (VLP) model for image-text matching. An iterative Grad-CAM refinement strategy is introduced to progressively enhance the model's focus on the target region and overcome positional insensitivity, creating a self-correcting effect. Additionally, we design the Primary Word Emphasis module to help the model handle complex semantic relations, enhancing its ability to attend to the intended object. Extensive experiments conducted on the RefCOCO/+/g, and PhraseCut benchmarks demonstrate that IteRPrimE outperforms previous state-of-the-art zero-shot methods, particularly excelling in out-of-domain scenarios.
One of the basic requirements of humans is clothing and this approach aims to identify the garments selected by customer during shopping, from surveillance video. The existing approaches to detect garments were developed on western wear using datasets of western clothing. They do not address Indian garments due to the increased complexity. In this work, we propose a computer vision based framework to address this problem through video surveillance. The proposed framework uses the Mixture of Gaussians background subtraction algorithm to identify the foreground present in a video frame. The visual information present in this foreground is analysed using computer vision techniques such as image segmentation to detect the various garments, the customer is interested in. The framework was tested on a dataset, that comprises of CCTV videos from a garments store. When presented with raw surveillance footage, the proposed framework demonstrated its effectiveness in detecting the interest of customer in choosing their garments by achieving a high precision and recall.
While numerous architectures for medical image segmentation have been proposed, achieving competitive performance with state-of-the-art models networks such as nnUNet, still leave room for further innovation. In this work, we introduce nnUZoo, an open source benchmarking framework built upon nnUNet, which incorporates various deep learning architectures, including CNNs, Transformers, and Mamba-based models. Using this framework, we provide a fair comparison to demystify performance claims across different medical image segmentation tasks. Additionally, in an effort to enrich the benchmarking, we explored five new architectures based on Mamba and Transformers, collectively named X2Net, and integrated them into nnUZoo for further evaluation. The proposed models combine the features of conventional U2Net, nnUNet, CNN, Transformer, and Mamba layers and architectures, called X2Net (UNETR2Net (UNETR), SwT2Net (SwinTransformer), SS2D2Net (SwinUMamba), Alt1DM2Net (LightUMamba), and MambaND2Net (MambaND)). We extensively evaluate the performance of different models on six diverse medical image segmentation datasets, including microscopy, ultrasound, CT, MRI, and PET, covering various body parts, organs, and labels. We compare their performance, in terms of dice score and computational efficiency, against their baseline models, U2Net, and nnUNet. CNN models like nnUNet and U2Net demonstrated both speed and accuracy, making them effective choices for medical image segmentation tasks. Transformer-based models, while promising for certain imaging modalities, exhibited high computational costs. Proposed Mamba-based X2Net architecture (SS2D2Net) achieved competitive accuracy with no significantly difference from nnUNet and U2Net, while using fewer parameters. However, they required significantly longer training time, highlighting a trade-off between model efficiency and computational cost.
While deep learning has significantly advanced medical image segmentation, most existing methods still struggle with handling complex anatomical regions. Cascaded or deep supervision-based approaches attempt to address this challenge through multi-scale feature learning but fail to establish sufficient inter-scale dependencies, as each scale relies solely on the features of the immediate predecessor. To this end, we propose the AutoRegressive Segmentation framework via next-scale mask prediction, termed AR-Seg, which progressively predicts the next-scale mask by explicitly modeling dependencies across all previous scales within a unified architecture. AR-Seg introduces three innovations: (1) a multi-scale mask autoencoder that quantizes the mask into multi-scale token maps to capture hierarchical anatomical structures, (2) a next-scale autoregressive mechanism that progressively predicts next-scale masks to enable sufficient inter-scale dependencies, and (3) a consensus-aggregation strategy that combines multiple sampled results to generate a more accurate mask, further improving segmentation robustness. Extensive experimental results on two benchmark datasets with different modalities demonstrate that AR-Seg outperforms state-of-the-art methods while explicitly visualizing the intermediate coarse-to-fine segmentation process.
Deep learning-based medical image segmentation typically requires large amount of labeled data for training, making it less applicable in clinical settings due to high annotation cost. Semi-supervised learning (SSL) has emerged as an appealing strategy due to its less dependence on acquiring abundant annotations from experts compared to fully supervised methods. Beyond existing model-centric advancements of SSL by designing novel regularization strategies, we anticipate a paradigmatic shift due to the emergence of promptable segmentation foundation models with universal segmentation capabilities using positional prompts represented by Segment Anything Model (SAM). In this paper, we present SemiSAM+, a foundation model-driven SSL framework to efficiently learn from limited labeled data for medical image segmentation. SemiSAM+ consists of one or multiple promptable foundation models as generalist models, and a trainable task-specific segmentation model as specialist model. For a given new segmentation task, the training is based on the specialist-generalist collaborative learning procedure, where the trainable specialist model delivers positional prompts to interact with the frozen generalist models to acquire pseudo-labels, and then the generalist model output provides the specialist model with informative and efficient supervision which benefits the automatic segmentation and prompt generation in turn. Extensive experiments on two public datasets and one in-house clinical dataset demonstrate that SemiSAM+ achieves significant performance improvement, especially under extremely limited annotation scenarios, and shows strong efficiency as a plug-and-play strategy that can be easily adapted to different specialist and generalist models.
Due to the domain shifts between training and testing medical images, learned segmentation models often experience significant performance degradation during deployment. In this paper, we first decompose an image into its style code and content map and reveal that domain shifts in medical images involve: \textbf{style shifts} (\emph{i.e.}, differences in image appearance) and \textbf{content shifts} (\emph{i.e.}, variations in anatomical structures), the latter of which has been largely overlooked. To this end, we propose \textbf{StyCona}, a \textbf{sty}le \textbf{con}tent decomposition-based data \textbf{a}ugmentation method that innovatively augments both image style and content within the rank-one space, for domain generalizable medical image segmentation. StyCona is a simple yet effective plug-and-play module that substantially improves model generalization without requiring additional training parameters or modifications to the segmentation model architecture. Experiments on cross-sequence, cross-center, and cross-modality medical image segmentation settings with increasingly severe domain shifts, demonstrate the effectiveness of StyCona and its superiority over state-of-the-arts. The code is available at https://github.com/Senyh/StyCona.
Weakly supervised segmentation methods can delineate thyroid nodules in ultrasound images efficiently using training data with coarse labels, but suffer from: 1) low-confidence pseudo-labels that follow topological priors, introducing significant label noise, and 2) low-rationality loss functions that rigidly compare segmentation with labels, ignoring discriminative information for nodules with diverse and complex shapes. To solve these issues, we clarify the objective and references for weakly supervised ultrasound image segmentation, presenting a framework with high-confidence pseudo-labels to represent topological and anatomical information and high-rationality losses to capture multi-level discriminative features. Specifically, we fuse geometric transformations of four-point annotations and MedSAM model results prompted by specific annotations to generate high-confidence box, foreground, and background labels. Our high-rationality learning strategy includes: 1) Alignment loss measuring spatial consistency between segmentation and box label, and topological continuity within the foreground label, guiding the network to perceive nodule location; 2) Contrastive loss pulling features from labeled foreground regions while pushing features from labeled foreground and background regions, guiding the network to learn nodule and background feature distribution; 3) Prototype correlation loss measuring consistency between correlation maps derived by comparing features with foreground and background prototypes, refining uncertain regions to accurate nodule edges. Experimental results show that our method achieves state-of-the-art performance on the TN3K and DDTI datasets. The code is available at https://github.com/bluehenglee/MLI-MSC.
Generalizable medical image segmentation is essential for ensuring consistent performance across diverse unseen clinical settings. However, existing methods often overlook the capability to generalize effectively across arbitrary unseen modalities. In this paper, we introduce a novel Test-Time Modality Generalization (TTMG) framework, which comprises two core components: Modality-Aware Style Projection (MASP) and Modality-Sensitive Instance Whitening (MSIW), designed to enhance generalization in arbitrary unseen modality datasets. The MASP estimates the likelihood of a test instance belonging to each seen modality and maps it onto a distribution using modality-specific style bases, guiding its projection effectively. Furthermore, as high feature covariance hinders generalization to unseen modalities, the MSIW is applied during training to selectively suppress modality-sensitive information while retaining modality-invariant features. By integrating MASP and MSIW, the TTMG framework demonstrates robust generalization capabilities for medical image segmentation in unseen modalities a challenge that current methods have largely neglected. We evaluated TTMG alongside other domain generalization techniques across eleven datasets spanning four modalities (colonoscopy, ultrasound, dermoscopy, and radiology), consistently achieving superior segmentation performance across various modality combinations.
The histogram of an image is the accurate graphical representation of the numerical grayscale distribution and it is also an estimate of the probability distribution of image pixels. Therefore, histogram has been widely adopted to calculate the clustering means and partitioning thresholds for image segmentation. There have been many classical histogram-based image segmentation methods proposed and played important roles in both academics and industry. In this tutorial, the histories and recent advances of the histogram-based image segmentation techniques are first reviewed and then they are divided into four categories: (1) the means-based method, (2) the Gaussian-mixture-model-based method, (3) the entropy-based method and (4) the feature-points-based method. The purpose of this tutorial is threefold: 1) to teach the principles of the classical histogram-based image segmentation methods to the interested readers; 2) to evaluate the advantages and disadvantages of these classical histogram-based image segmentation methods objectively; 3) to compare the performances of these classical histogram-based image segmentation methods with state-of-the-art deep learning based methods objectively.
Analyzing imaging and hyperspectral data is crucial across scientific fields, including biology, medicine, chemistry, and physics. The primary goal is to transform high-resolution or high-dimensional data into an interpretable format to generate actionable insights, aiding decision-making and advancing knowledge. Currently, this task relies on complex, human-designed workflows comprising iterative steps such as denoising, spatial sampling, keypoint detection, feature generation, clustering, dimensionality reduction, and physics-based deconvolutions. The introduction of machine learning over the past decade has accelerated tasks like image segmentation and object detection via supervised learning, and dimensionality reduction via unsupervised methods. However, both classical and NN-based approaches still require human input, whether for hyperparameter tuning, data labeling, or both. The growing use of automated imaging tools, from atomically resolved imaging to biological applications, demands unsupervised methods that optimize data representation for human decision-making or autonomous experimentation. Here, we discuss advances in reward-based workflows, which adopt expert decision-making principles and demonstrate strong transfer learning across diverse tasks. We represent image analysis as a decision-making process over possible operations and identify desiderata and their mappings to classical decision-making frameworks. Reward-driven workflows enable a shift from supervised, black-box models sensitive to distribution shifts to explainable, unsupervised, and robust optimization in image analysis. They can function as wrappers over classical and DCNN-based methods, making them applicable to both unsupervised and supervised workflows (e.g., classification, regression for structure-property mapping) across imaging and hyperspectral data.
Indonesia is rich in languages and scripts. However, most NLP progress has been made using romanized text. In this paper, we present NusaAksara, a novel public benchmark for Indonesian languages that includes their original scripts. Our benchmark covers both text and image modalities and encompasses diverse tasks such as image segmentation, OCR, transliteration, translation, and language identification. Our data is constructed by human experts through rigorous steps. NusaAksara covers 8 scripts across 7 languages, including low-resource languages not commonly seen in NLP benchmarks. Although unsupported by Unicode, the Lampung script is included in this dataset. We benchmark our data across several models, from LLMs and VLMs such as GPT-4o, Llama 3.2, and Aya 23 to task-specific systems such as PP-OCR and LangID, and show that most NLP technologies cannot handle Indonesia's local scripts, with many achieving near-zero performance.
Medical image segmentation is crucial for clinical diagnosis and treatment planning, especially when dealing with complex anatomical structures such as vessels. However, accurately segmenting vessels remains challenging due to their small size, intricate edge structures, and susceptibility to artifacts and imaging noise. In this work, we propose VesselSAM, an enhanced version of the Segment Anything Model (SAM), specifically tailored for aortic vessel segmentation. VesselSAM incorporates AtrousLoRA, a novel module integrating Atrous Attention and Low-Rank Adaptation (LoRA), to enhance segmentation performance. Atrous Attention enables the model to capture multi-scale contextual information, preserving both fine-grained local details and broader global context. Additionally, LoRA facilitates efficient fine-tuning of the frozen SAM image encoder, reducing the number of trainable parameters and thereby enhancing computational efficiency. We evaluate VesselSAM using two challenging datasets: the Aortic Vessel Tree (AVT) dataset and the Type-B Aortic Dissection (TBAD) dataset. VesselSAM achieves state-of-the-art performance, attaining DSC scores of 93.50\%, 93.25\%, 93.02\%, and 93.26\% across multi-center datasets. Our results demonstrate that VesselSAM delivers high segmentation accuracy while significantly reducing computational overhead compared to existing large-scale models. This development paves the way for enhanced AI-based aortic vessel segmentation in clinical environments. The code and models will be released at https://github.com/Adnan-CAS/AtrousLora.
We formulate truncated singular value decompositions of entire convolutional neural networks. We demonstrate the computed left and right singular vectors are useful in identifying which images the convolutional neural network is likely to perform poorly on. To create this diagnostic tool, we define two metrics: the Right Projection Ratio and the Left Projection Ratio. The Right (Left) Projection Ratio evaluates the fidelity of the projection of an image (label) onto the computed right (left) singular vectors. We observe that both ratios are able to identify the presence of class imbalance for an image classification problem. Additionally, the Right Projection Ratio, which only requires unlabeled data, is found to be correlated to the model's performance when applied to image segmentation. This suggests the Right Projection Ratio could be a useful metric to estimate how likely the model is to perform well on a sample.
Medical Hyperspectral Imaging (MHSI) offers potential for computational pathology and precision medicine. However, existing CNN and Transformer struggle to balance segmentation accuracy and speed due to high spatial-spectral dimensionality. In this study, we leverage Mamba's global context modeling to propose a dual-stream architecture for joint spatial-spectral feature extraction. To address the limitation of Mamba's unidirectional aggregation, we introduce a recurrent spectral sequence representation to capture low-redundancy global spectral features. Experiments on a public Multi-Dimensional Choledoch dataset and a private Cervical Cancer dataset show that our method outperforms state-of-the-art approaches in segmentation accuracy while minimizing resource usage and achieving the fastest inference speed. Our code will be available at https://github.com/DeepMed-Lab-ECNU/MDN.
Domain shift presents a significant challenge in applying Deep Learning to the segmentation of 3D medical images from sources like Magnetic Resonance Imaging (MRI) and Computed Tomography (CT). Although numerous Domain Adaptation methods have been developed to address this issue, they are often evaluated under impractical data shift scenarios. Specifically, the medical imaging datasets used are often either private, too small for robust training and evaluation, or limited to single or synthetic tasks. To overcome these limitations, we introduce a M3DA /"mEd@/ benchmark comprising four publicly available, multiclass segmentation datasets. We have designed eight domain pairs featuring diverse and practically relevant distribution shifts. These include inter-modality shifts between MRI and CT and intra-modality shifts among various MRI acquisition parameters, different CT radiation doses, and presence/absence of contrast enhancement in images. Within the proposed benchmark, we evaluate more than ten existing domain adaptation methods. Our results show that none of them can consistently close the performance gap between the domains. For instance, the most effective method reduces the performance gap by about 62% across the tasks. This highlights the need for developing novel domain adaptation algorithms to enhance the robustness and scalability of deep learning models in medical imaging. We made our M3DA benchmark publicly available: https://github.com/BorisShirokikh/M3DA.
Supervised deep learning usually faces more challenges in medical images than in natural images. Since annotations in medical images require the expertise of doctors and are more time-consuming and expensive. Thus, some researchers turn to unsupervised learning methods, which usually face inevitable performance drops. In addition, medical images may have been acquired at different medical centers with different scanners and under different image acquisition protocols, so the modalities of the medical images are often inconsistent. This modality difference (domain shift) also reduces the applicability of deep learning methods. In this regard, we propose an unsupervised crossmodality domain adaptation method based on image translation by transforming the source modality image with annotation into the unannotated target modality and using its annotation to achieve supervised learning of the target modality. In addition, the subtle differences between translated pseudo images and real images are overcome by self-training methods to further improve the task performance of deep learning. The proposed method showed mean Dice Similarity Coefficient (DSC) and Average Symmetric Surface Distance (ASSD) of $0.8351 \pm 0.1152$ and $1.6712 \pm 2.1948$ for vestibular schwannoma (VS), $0.8098 \pm 0.0233$ and $0.2317 \pm 0.1577$ for cochlea on the VS and cochlea segmentation task of the Cross-Modality Domain Adaptation (crossMoDA 2022) challenge validation phase leaderboard.
As a novel and challenging task, referring segmentation combines computer vision and natural language processing to localize and segment objects based on textual descriptions. While referring image segmentation (RIS) has been extensively studied in natural images, little attention has been given to aerial imagery, particularly from unmanned aerial vehicles (UAVs). The unique challenges of UAV imagery, including complex spatial scales, occlusions, and varying object orientations, render existing RIS approaches ineffective. A key limitation has been the lack of UAV-specific datasets, as manually annotating pixel-level masks and generating textual descriptions is labour-intensive and time-consuming. To address this gap, we design an automatic labelling pipeline that leverages pre-existing UAV segmentation datasets and Multimodal Large Language Models (MLLM) for generating textual descriptions. Furthermore, we propose Aerial Referring Transformer (AeroReformer), a novel framework for UAV referring image segmentation (UAV-RIS), featuring a Vision-Language Cross-Attention Module (VLCAM) for effective cross-modal understanding and a Rotation-Aware Multi-Scale Fusion (RAMSF) decoder to enhance segmentation accuracy in aerial scenes. Extensive experiments on two newly developed datasets demonstrate the superiority of AeroReformer over existing methods, establishing a new benchmark for UAV-RIS. The datasets and code will be publicly available at: https://github.com/lironui/AeroReformer.
Over the last decade, the use of machine learning (ML) approaches in medicinal applications has increased manifold. Most of these approaches are based on deep learning, which aims to learn representations from grid data (like medical images). However, reinforcement learning (RL) applications in medicine are relatively less explored. Medical applications often involve a sequence of subtasks that form a diagnostic pipeline, and RL is uniquely suited to optimize over such sequential decision-making tasks. Ultrasound (US) image analysis is a quintessential example of such a sequential decision-making task, where the raw signal captured by the US transducer undergoes a series of signal processing and image post-processing steps, generally leading to a diagnostic suggestion. The application of RL in US remains limited. Deep Reinforcement Learning (DRL), that combines deep learning and RL, holds great promise in optimizing these pipelines by enabling intelligent and sequential decision-making. This review paper surveys the applications of RL in US over the last decade. We provide a succinct overview of the theoretic framework of RL and its application in US image processing and review existing work in each aspect of the image analysis pipeline. A comprehensive search of Scopus filtered on relevance yielded 14 papers most relevant to this topic. These papers were further categorized based on their target applications image classification, image segmentation, image enhancement, video summarization, and auto navigation and path planning. We also examined the type of RL approach used in each publication. Finally, we discuss key areas in healthcare where DRL approaches in US could be used for sequential decision-making. We analyze the opportunities, challenges, and limitations, providing insights into the future potential of DRL in US image analysis.