Medical image sequences, generated by both 2D video-based examinations and 3D imaging techniques, consist of sequential frames or slices that capture the same anatomical entities (e.g., organs or lesions) from multiple perspectives. Existing segmentation studies typically process medical images using either 2D or 3D methods in isolation, often overlooking the inherent consistencies among these images. Additionally, interactive segmentation, while highly beneficial in clinical scenarios, faces the challenge of integrating text prompts effectively across multi-modalities. To address these issues, we introduce an innovative task, Referring Medical Image Sequence Segmentation for the first time, which aims to segment the referred anatomical entities corresponding to medical text prompts. We develop a strong baseline model, Text-Promptable Propagation (TPP), designed to exploit the intrinsic relationships among sequential images and their associated textual descriptions. TPP supports the segmentation of arbitrary objects of interest based on cross-modal prompt fusion. Carefully designed medical prompts are fused and employed as queries to guide image sequence segmentation through triple-propagation. We curate a large and comprehensive benchmark covering 4 modalities and 20 different organs and lesions. Experimental results consistently demonstrate the superior performance of our approach compared to previous methods across these datasets.
Semi-supervised 3D medical image segmentation aims to achieve accurate segmentation using few labelled data and numerous unlabelled data. The main challenge in the design of semi-supervised learning methods consists in the effective use of the unlabelled data for training. A promising solution consists of ensuring consistent predictions across different views of the data, where the efficacy of this strategy depends on the accuracy of the pseudo-labels generated by the model for this consistency learning strategy. In this paper, we introduce a new methodology to produce high-quality pseudo-labels for a consistency learning strategy to address semi-supervised 3D medical image segmentation. The methodology has three important contributions. The first contribution is the Cooperative Rectification Learning Network (CRLN) that learns multiple prototypes per class to be used as external knowledge priors to adaptively rectify pseudo-labels at the voxel level. The second contribution consists of the Dynamic Interaction Module (DIM) to facilitate pairwise and cross-class interactions between prototypes and multi-resolution image features, enabling the production of accurate voxel-level clues for pseudo-label rectification. The third contribution is the Cooperative Positive Supervision (CPS), which optimises uncertain representations to align with unassertive representations of their class distributions, improving the model's accuracy in classifying uncertain regions. Extensive experiments on three public 3D medical segmentation datasets demonstrate the effectiveness and superiority of our semi-supervised learning method.
Deep learning (DL) techniques have emerged as promising solutions for medical wound tissue segmentation. However, a notable limitation in this field is the lack of publicly available labelled datasets and a standardised performance evaluation of state-of-the-art DL models on such datasets. This study addresses this gap by comprehensively evaluating various DL models for wound tissue segmentation using a novel dataset. We have curated a dataset comprising 147 wound images exhibiting six tissue types: slough, granulation, maceration, necrosis, bone, and tendon. The dataset was meticulously labelled for semantic segmentation employing supervised machine learning techniques. Three distinct labelling formats were developed -- full image, patch, and superpixel. Our investigation encompassed a wide array of DL segmentation and classification methodologies, ranging from conventional approaches like UNet, to generative adversarial networks such as cGAN, and modified techniques like FPN+VGG16. Also, we explored DL-based classification methods (e.g., ResNet50) and machine learning-based classification leveraging DL features (e.g., AlexNet+RF). In total, 82 wound tissue segmentation models were derived across the three labelling formats. Our analysis yielded several notable findings, including identifying optimal DL models for each labelling format based on weighted average Dice or F1 scores. Notably, FPN+VGG16 emerged as the top-performing DL model for wound tissue segmentation, achieving a dice score of 82.25%. This study provides a valuable benchmark for evaluating wound image segmentation and classification models, offering insights to inform future research and clinical practice in wound care. The labelled dataset created in this study is available at https://github.com/akabircs/WoundTissue.
Accurate morphometric assessment of cartilage-such as thickness/volume-via MRI is essential for monitoring knee osteoarthritis. Segmenting cartilage remains challenging and dependent on extensive expert-annotated datasets, which are heavily subjected to inter-reader variability. Recent advancements in Visual Foundational Models (VFM), especially memory-based approaches, offer opportunities for improving generalizability and robustness. This study introduces a deep learning (DL) method for cartilage and meniscus segmentation from 3D MRIs using interactive, memory-based VFMs. To improve spatial awareness and convergence, we incorporated a Hybrid Shuffling Strategy (HSS) during training and applied a segmentation mask propagation technique to enhance annotation efficiency. We trained four AI models-a CNN-based 3D-VNet, two automatic transformer-based models (SaMRI2D and SaMRI3D), and a transformer-based promptable memory-based VFM (SAMRI-2)-on 3D knee MRIs from 270 patients using public and internal datasets and evaluated on 57 external cases, including multi-radiologist annotations and different data acquisitions. Model performance was assessed against reference standards using Dice Score (DSC) and Intersection over Union (IoU), with additional morphometric evaluations to further quantify segmentation accuracy. SAMRI-2 model, trained with HSS, outperformed all other models, achieving an average DSC improvement of 5 points, with a peak improvement of 12 points for tibial cartilage. It also demonstrated the lowest cartilage thickness errors, reducing discrepancies by up to threefold. Notably, SAMRI-2 maintained high performance with as few as three user clicks per volume, reducing annotation effort while ensuring anatomical precision. This memory-based VFM with spatial awareness offers a novel approach for reliable AI-assisted knee MRI segmentation, advancing DL in musculoskeletal imaging.
Deep learning-based medical image analysis faces a significant barrier due to the lack of interpretability. Conventional explainable AI (XAI) techniques, such as Grad-CAM and SHAP, often highlight regions outside clinical interests. To address this issue, we propose Segmentation-based Explanation (SegX), a plug-and-play approach that enhances interpretability by aligning the model's explanation map with clinically relevant areas leveraging the power of segmentation models. Furthermore, we introduce Segmentation-based Uncertainty Assessment (SegU), a method to quantify the uncertainty of the prediction model by measuring the 'distance' between interpretation maps and clinically significant regions. Our experiments on dermoscopic and chest X-ray datasets show that SegX improves interpretability consistently across mortalities, and the certainty score provided by SegU reliably reflects the correctness of the model's predictions. Our approach offers a model-agnostic enhancement to medical image diagnosis towards reliable and interpretable AI in clinical decision-making.
Background: Computed Tomography Angiography (CTA) is crucial for cerebrovascular disease diagnosis. Dynamic CTA is a type of imaging that captures temporal information about the We aim to develop and evaluate two segmentation techniques to segment vessels directly on CTA images: (1) creating and registering population-averaged vessel atlases and (2) using deep learning (DL). Methods: We retrieved 4D-CT of the head from our institutional research database, with bone and soft tissue subtracted from post-contrast images. An Advanced Normalization Tools pipeline was used to create angiographic atlases from 25 patients. Then, atlas-driven ROIs were identified by a CT attenuation threshold to generate segmentation of the arteries and veins using non-linear registration. To create DL vessel segmentations, arterial and venous structures were segmented using the MRA vessel segmentation tool, iCafe, in 29 patients. These were then used to train a DL model, with bone-in CT images as input. Multiple phase images in the 4D-CT were used to increase the training and validation dataset. Both segmentation approaches were evaluated on a test 4D-CT dataset of 11 patients which were also processed by iCafe and validated by a neuroradiologist. Specifically, branch-wise segmentation accuracy was quantified with 20 labels for arteries and one for veins. DL outperformed the atlas-based segmentation models for arteries (average modified dice coefficient (amDC) 0.856 vs. 0.324) and veins (amDC 0.743 vs. 0.495) overall. For ICAs, vertebral and basilar arteries, DL and atlas -based segmentation had an amDC of 0.913 and 0.402, respectively. The amDC for MCA-M1, PCA-P1, and ACA-A1 segments were 0.932 and 0.474, respectively. Conclusion: Angiographic CT templates are developed for the first time in literature. Using 4D-CTA enables the use of tools like iCafe, lessening the burden of manual annotation.
The bicuspid aortic valve (BAV) is the most prevalent congenital heart defect and may require surgery for complications such as stenosis, regurgitation, and aortopathy. BAV repair surgery is effective but challenging due to the heterogeneity of BAV morphology. Multiple imaging modalities can be employed to assist the quantitative assessment of BAVs for surgical planning. Contrast-enhanced 4D computed tomography (CT) produces volumetric temporal sequences with excellent contrast and spatial resolution. Segmentation of the aortic cusps and root in these images is an essential step in creating patient specific models for visualization and quantification. While deep learning-based methods are capable of fully automated segmentation, no BAV-specific model exists. Among valve segmentation studies, there has been limited quantitative assessment of the clinical usability of the segmentation results. In this work, we developed a fully auto- mated multi-label BAV segmentation pipeline based on nnU-Net. The predicted segmentations were used to carry out surgically relevant morphological measurements including geometric cusp height, commissural angle and annulus diameter, and the results were compared against manual segmentation. Automated segmentation achieved average Dice scores of over 0.7 and symmetric mean distance below 0.7 mm for all three aortic cusps and the root wall. Clinically relevant benchmarks showed good consistency between manual and predicted segmentations. Overall, fully automated BAV segmentation of 3D frames in 4D CT can produce clinically usable measurements for surgical risk stratification, but the temporal consistency of segmentations needs to be improved.
Body composition assessment using CT images can potentially be used for a number of clinical applications, including the prognostication of cardiovascular outcomes, evaluation of metabolic health, monitoring of disease progression, assessment of nutritional status, prediction of treatment response in oncology, and risk stratification for surgical and critical care outcomes. While multiple groups have developed in-house segmentation tools for this analysis, there are very limited publicly available tools that could be consistently used across different applications. To mitigate this gap, we present a publicly accessible, end-to-end segmentation and feature calculation model specifically for CT body composition analysis. Our model performs segmentation of skeletal muscle, subcutaneous adipose tissue (SAT), and visceral adipose tissue (VAT) across the chest, abdomen, and pelvis area in axial CT images. It also provides various body composition metrics, including muscle density, visceral-to-subcutaneous fat (VAT/SAT) ratio, muscle area/volume, and skeletal muscle index (SMI), supporting both 2D and 3D assessments. To evaluate the model, the segmentation was applied to both internal and external datasets, with body composition metrics analyzed across different age, sex, and race groups. The model achieved high dice coefficients on both internal and external datasets, exceeding 89% for skeletal muscle, SAT, and VAT segmentation. The model outperforms the benchmark by 2.40% on skeletal muscle and 10.26% on SAT compared to the manual annotations given by the publicly available dataset. Body composition metrics show mean relative absolute errors (MRAEs) under 10% for all measures. Furthermore, the model provided muscular fat segmentation with a Dice coefficient of 56.27%, which can be utilized for additional analyses as needed.
The recent Segment Anything Models (SAMs) have emerged as foundational visual models for general interactive segmentation. Despite demonstrating robust generalization abilities, they still suffer performance degradations in scenarios demanding accurate masks. Existing methods for high-precision interactive segmentation face a trade-off between the ability to perceive intricate local details and maintaining stable prompting capability, which hinders the applicability and effectiveness of foundational segmentation models. To this end, we present an SAM2Refiner framework built upon the SAM2 backbone. This architecture allows SAM2 to generate fine-grained segmentation masks for both images and videos while preserving its inherent strengths. Specifically, we design a localization augment module, which incorporates local contextual cues to enhance global features via a cross-attention mechanism, thereby exploiting potential detailed patterns and maintaining semantic information. Moreover, to strengthen the prompting ability toward the enhanced object embedding, we introduce a prompt retargeting module to renew the embedding with spatially aligned prompt features. In addition, to obtain accurate high resolution segmentation masks, a mask refinement module is devised by employing a multi-scale cascaded structure to fuse mask features with hierarchical representations from the encoder. Extensive experiments demonstrate the effectiveness of our approach, revealing that the proposed method can produce highly precise masks for both images and videos, surpassing state-of-the-art methods.
Purpose: Foundation models, trained on multitudes of public datasets, often require additional fine-tuning or re-prompting mechanisms to be applied to visually distinct target domains such as surgical videos. Further, without domain knowledge, they cannot model the specific semantics of the target domain. Hence, when applied to surgical video segmentation, they fail to generalise to sections where previously tracked objects leave the scene or new objects enter. Methods: We propose SASVi, a novel re-prompting mechanism based on a frame-wise Mask R-CNN Overseer model, which is trained on a minimal amount of scarcely available annotations for the target domain. This model automatically re-prompts the foundation model SAM2 when the scene constellation changes, allowing for temporally smooth and complete segmentation of full surgical videos. Results: Re-prompting based on our Overseer model significantly improves the temporal consistency of surgical video segmentation compared to similar prompting techniques and especially frame-wise segmentation, which neglects temporal information, by at least 1.5%. Our proposed approach allows us to successfully deploy SAM2 to surgical videos, which we quantitatively and qualitatively demonstrate for three different cholecystectomy and cataract surgery datasets. Conclusion: SASVi can serve as a new baseline for smooth and temporally consistent segmentation of surgical videos with scarcely available annotation data. Our method allows us to leverage scarce annotations and obtain complete annotations for full videos of the large-scale counterpart datasets. We make those annotations publicly available, providing extensive annotation data for the future development of surgical data science models.
Accurate segmentation of all pathological findings in 3D medical images remains a significant challenge, as supervised models are limited to detecting only the few pathology classes annotated in existing datasets. To address this, we frame pathology segmentation as an unsupervised visual anomaly segmentation (UVAS) problem, leveraging the inherent rarity of pathological patterns compared to healthy ones. We enhance the existing density-based UVAS framework with two key innovations: (1) dense self-supervised learning (SSL) for feature extraction, eliminating the need for supervised pre-training, and (2) learned, masking-invariant dense features as conditioning variables, replacing hand-crafted positional encodings. Trained on over 30,000 unlabeled 3D CT volumes, our model, Screener, outperforms existing UVAS methods on four large-scale test datasets comprising 1,820 scans with diverse pathologies. Code and pre-trained models will be made publicly available.
Existing visual perception systems focus on region-level segmentation in single-turn dialogues, relying on complex and explicit query instructions. Such systems cannot reason at the pixel level and comprehend dynamic user intent that changes over interaction. Our work tackles this issue by introducing a novel task, Pixel-level Reasoning Segmentation (Pixel-level RS) based on multi-turn conversations, tracking evolving user intent via multi-turn interactions for fine-grained segmentation. To establish a benchmark for this novel task, we build a Pixel-level ReasonIng Segmentation Dataset Based on Multi-Turn Conversations (PRIST), comprising 24k utterances from 8.3k multi-turn conversational scenarios with segmentation targets. Building on PRIST, we further propose MIRAS, a Multi-turn Interactive ReAsoning Segmentation framework, integrates pixel-level segmentation with robust multi-turn conversation understanding, generating pixel-grounded explanations aligned with user intent. The PRIST dataset and MIRSA framework fill the gap in pixel-level reasoning segmentation. Experimental results on the PRIST dataset demonstrate that our method outperforms current segmentation-specific baselines in terms of segmentation and LLM-based reasoning metrics. The code and data are available at: https://github.com/ccccai239/PixelRIST.
Existing models typically segment either the entire 3D frame or 2D slices independently to derive clinical functional metrics from ventricular segmentation in cardiac cine sequences. While performing well overall, they struggle at the end slices. To address this, we leverage spatial continuity to extract global uncertainty from segmentation variance and use it as memory in our ensemble learning method, Streaming, for classifier weighting, balancing overall and end-slice performance. Additionally, we introduce the End Coefficient (EC) to quantify end-slice accuracy. Experiments on ACDC and M\&Ms datasets show that our framework achieves near-state-of-the-art Dice Similarity Coefficient (DSC) and outperforms all models on end-slice performance, improving patient-specific segmentation accuracy.
The hemorrhagic lesion segmentation plays a critical role in ophthalmic diagnosis, directly influencing early disease detection, treatment planning, and therapeutic efficacy evaluation. However, the task faces significant challenges due to lesion morphological variability, indistinct boundaries, and low contrast with background tissues. To improve diagnostic accuracy and treatment outcomes, developing advanced segmentation techniques remains imperative. This paper proposes an adversarial learning-based dynamic architecture adjustment approach that integrates hierarchical U-shaped encoder-decoder, residual blocks, attention mechanisms, and ASPP modules. By dynamically optimizing feature fusion, our method enhances segmentation performance. Experimental results demonstrate a Dice coefficient of 0.6802, IoU of 0.5602, Recall of 0.766, Precision of 0.6525, and Accuracy of 0.9955, effectively addressing the challenges in fundus image hemorrhage segmentation.[* Corresponding author.]
Segmentation of Hypoxic-Ischemic Encephalopathy (HIE) lesions in neonatal MRI is a crucial but challenging task due to diffuse multifocal lesions with varying volumes and the limited availability of annotated HIE lesion datasets. Using the BONBID-HIE dataset, we implemented a 3D U-Net with optimized preprocessing, augmentation, and training strategies to overcome data constraints. The goal of this study is to identify the optimal loss function specifically for the HIE lesion segmentation task. To this end, we evaluated various loss functions, including Dice, Dice-Focal, Tversky, Hausdorff Distance (HausdorffDT) Loss, and two proposed compound losses -- Dice-Focal-HausdorffDT and Tversky-HausdorffDT -- to enhance segmentation performance. The results show that different loss functions predict distinct segmentation masks, with compound losses outperforming standalone losses. Tversky-HausdorffDT Loss achieves the highest Dice and Normalized Surface Dice scores, while Dice-Focal-HausdorffDT Loss minimizes Mean Surface Distance. This work underscores the significance of task-specific loss function optimization, demonstrating that combining region-based and boundary-aware losses leads to more accurate HIE lesion segmentation, even with limited training data.
Extracting specific items from 10-K reports remains challenging due to variations in document formats and item presentation. Traditional rule-based item segmentation approaches often yield suboptimal results. This study introduces two advanced item segmentation methods leveraging language models: (1) GPT4ItemSeg, using a novel line-ID-based prompting mechanism to utilize GPT4 for item segmentation, and (2) BERT4ItemSeg, combining BERT embeddings with a Bi-LSTM model in a hierarchical structure to overcome context window constraints. Trained and evaluated on 3,737 annotated 10-K reports, BERT4ItemSeg achieved a macro-F1 of 0.9825, surpassing GPT4ItemSeg (0.9567), conditional random field (0.9818), and rule-based methods (0.9048) for core items (1, 1A, 3, and 7). These approaches enhance item segmentation performance, improving text analytics in accounting and finance. BERT4ItemSeg offers satisfactory item segmentation performance, while GPT4ItemSeg can easily adapt to regulatory changes. Together, they offer practical benefits for researchers and practitioners, enabling reliable empirical studies and automated 10-K item segmentation functionality.
Automated lesion segmentation of medical images has made tremendous improvements in recent years due to deep learning advancements. However, accurately capturing fine-grained global and regional feature representations remains a challenge. Many existing methods obtain suboptimal performance on complex lesion segmentation due to information loss during typical downsampling operations and the insufficient capture of either regional or global features. To address these issues, we propose the Global and Regional Compensation Segmentation Framework (GRCSF), which introduces two key innovations: the Global Compensation Unit (GCU) and the Region Compensation Unit (RCU). The proposed GCU addresses resolution loss in the U-shaped backbone by preserving global contextual features and fine-grained details during multiscale downsampling. Meanwhile, the RCU introduces a self-supervised learning (SSL) residual map generated by Masked Autoencoders (MAE), obtained as pixel-wise differences between reconstructed and original images, to highlight regions with potential lesions. These SSL residual maps guide precise lesion localization and segmentation through a patch-based cross-attention mechanism that integrates regional spatial and pixel-level features. Additionally, the RCU incorporates patch-level importance scoring to enhance feature fusion by leveraging global spatial information from the backbone. Experiments on two publicly available medical image segmentation datasets, including brain stroke lesion and coronary artery calcification datasets, demonstrate that our GRCSF outperforms state-of-the-art methods, confirming its effectiveness across diverse lesion types and its potential as a generalizable lesion segmentation solution.
Differentiating signals from the background in micrographs is a critical initial step for cryogenic electron microscopy (cryo-EM), yet it remains laborious due to low signal-to-noise ratio (SNR), the presence of contaminants and densely packed particles of varying sizes. Although image segmentation has recently been introduced to distinguish particles at the pixel level, the low SNR complicates the automated generation of accurate annotations for training supervised models. Moreover, platforms for systematically comparing different design choices in pipeline construction are lacking. Thus, a modular framework is essential to understand the advantages and limitations of this approach and drive further development. To address these challenges, we present a pipeline that automatically generates high-quality segmentation maps from cryo-EM data to serve as ground truth labels. Our modular framework enables the selection of various segmentation models and loss functions. We also integrate Conditional Random Fields (CRFs) with different solvers and feature sets to refine coarse predictions, thereby producing fine-grained segmentation. This flexibility facilitates optimal configurations tailored to cryo-EM datasets. When trained on a limited set of micrographs, our approach achieves over 90% accuracy, recall, precision, Intersection over Union (IoU), and F1-score on synthetic data. Furthermore, to demonstrate our framework's efficacy in downstream analyses, we show that the particles extracted by our pipeline produce 3D density maps with higher resolution than those generated by existing particle pickers on real experimental datasets, while achieving performance comparable to that of manually curated datasets from experts.
This work introduces Semantically Masked VQ-GAN (SQ-GAN), a novel approach integrating generative models to optimize image compression for semantic/task-oriented communications. SQ-GAN employs off-the-shelf semantic semantic segmentation and a new specifically developed semantic-conditioned adaptive mask module (SAMM) to selectively encode semantically significant features of the images. SQ-GAN outperforms state-of-the-art image compression schemes such as JPEG2000 and BPG across multiple metrics, including perceptual quality and semantic segmentation accuracy on the post-decoding reconstructed image, at extreme low compression rates expressed in bits per pixel.
Sketch segmentation involves grouping pixels within a sketch that belong to the same object or instance. It serves as a valuable tool for sketch editing tasks, such as moving, scaling, or removing specific components. While image segmentation models have demonstrated remarkable capabilities in recent years, sketches present unique challenges for these models due to their sparse nature and wide variation in styles. We introduce InkLayer, a method for instance segmentation of raster scene sketches. Our approach adapts state-of-the-art image segmentation and object detection models to the sketch domain by employing class-agnostic fine-tuning and refining segmentation masks using depth cues. Furthermore, our method organizes sketches into sorted layers, where occluded instances are inpainted, enabling advanced sketch editing applications. As existing datasets in this domain lack variation in sketch styles, we construct a synthetic scene sketch segmentation dataset, InkScenes, featuring sketches with diverse brush strokes and varying levels of detail. We use this dataset to demonstrate the robustness of our approach.