Multi Organ Computed Tomography Segmentation

Follow this topic Ask about this topic

Momentum

5 papers in the last four weeks, against 2 the four weeks before. 0.1% of all new papers.

Jul 6Week of Sep 21

Latest papers 52

Sep 22, 2026cs.CV

FleXray: Universal Clinical X-ray Segmentation

X-ray is medicine's most widely used imaging modality, yet remains among its least quantitative. Unlike volumetric modalities like CT or MRI, X-ray collapses 3D anatomy into a 2D projection, causing structures to overlap and anatomical boundaries to be ambiguous, even to experts. As a result, labeling X-ray databases for training general-purpose segmentation systems is impractical, leaving morphometric and functional X-ray analysis confined to narrow anatomical regions and applications. To this end, we present FleXray, a generalist model for anatomical segmentation across the entire body in clinical X-rays. Instead of curating large, manually annotated X-ray datasets, we build a scalable, physics-based generative X-ray data engine. Using existing 3D whole-body CT segmentation datasets and generative image-editing models, we simulate fully-annotated 2D X-rays with diverse appearances, physiological properties, and imaging geometries. Trained on these simulations, FleXray accurately segments 60 anatomical structures across unseen research datasets and in-the-wild X-rays. We further show that FleXray makes X-rays directly amenable to quantitative analysis, enabling automated measurements for disease grading, robust navigation during X-ray-guided interventions, and data-efficient learning of pathological targets. We release the model, code, a full-body X-ray segmentation dataset, and a local, easy-to-use browser-based tool at https://flexray.csail.mit.edu .

Victor Ion Butoi, Vivek Gopalakrishnan, John V. Guttag +2

MIT CSAIL · Massachusetts General Hospital · Harvard Medical School

X-Ray Multi Organ Computed Tomography Segmentation X-Ray Photon Correlation Spectroscopy Anatomy

Sep 21, 2026cs.CV

FedMust: Semi-supervised Multi-task Student-Teacher Federated Learning for Multi-organ CT Segmentation

Multi-organ segmentation using deep learning requires large amounts of annotated patient data; however, institutions often lack sufficiently large and diverse annotated datasets. Privacy constraints further prevent institutions from sharing patient data to overcome this limitation. Moreover, due to the labor-intensive nature of annotation and the scarcity of diverse expertise, institutions typically have labels for only a small portion of their local data, leaving the larger unlabeled portion unused. In this work, we propose a flexible semi-supervised federated multi-task student-teacher framework that leverages federated learning (FL) to improve multi-organ segmentation using both labeled and unlabeled data across participating sites. At each communication round, the proposed framework initiates local training, where clients with labels for the same task form a federation to produce an aggregated teacher model. The resulting teachers generate task-specific features for all data at each client. Subsequently, all clients form a second federation to train a multi-task student model with a shared encoder and task-specific decoders that replicate the teacher-generated features across all segmentation tasks. The aggregated student model is then used to update the local teachers and initiate the next training round. Extensive experiments demonstrated the effectiveness of the proposed method compared with local and federated single-organ models, yielding an average performance gain of 13 percent across clients. The experiments also demonstrated the impact of multi-task learning and unlabeled data and the applicability of the framework in relaxing labeled-data requirements for client participation. The code is available at https://github.com/AshknMrd/FedMust.

Ashkan Moradi, Bendik Skarre Abrahamsen, Mattijs Elschot

Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway · Central Staff at St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway

Semi-Supervised Medical Image Segmentation Multi Organ Computed Tomography Segmentation Multi--Task Learning Fedavg Encoders

Sep 21, 2026cs.CV

DiaSeg: Diagonal Segment Extraction from DTW Paths for Interpretable Gait Analysis

Dynamic Time Warping (DTW) is the dominant approach for measuring similarity between time series, yet standard practice discards the optimal warping path after computing a single distance value, losing local alignment information most relevant to clinical diagnosis. We introduce DiaSeg, a framework that extracts diagonal segments from DTW paths with controlled breaks, characterizing each segment by five geometric features (effective length, interruption count, cost variation, temporal position, and path context), and enabling unsupervised pattern discovery without domain-specific feature engineering. Validated on 91 subjects across six clinical conditions (healthy aging, Parkinson's, Huntington's, ALS, brain tumor, and stroke), three findings emerge. First, diagonal segments form consistent unsupervised patterns (silhouette 0.33) aligned with biomechanical phase annotations, with label-based validation confirming near-perfect separation of healthy and pathological gait (ARI up to 0.986). Second, segments discriminate pathology at 69% (supervised) and 75% (patient-level clustering), with pathology manifesting through distributional shifts in segment length; combining segment and cycle-level features further improves classification to 91.7%. Third, while cycle-based methods achieve higher accuracy (91%), diagonal segments provide phase-specific interpretability unavailable in global representations, localizing where coordination breaks down within the gait cycle. DiaSeg thus transforms DTW from a black-box distance into a source of interpretable temporal features for neurodegenerative disease assessment.

Tresor Y. Koffi, Amel Hidouri, Corentin Legrand +1

Université Bourgogne Europe, CIAD UR 7533, Dijon, 21000, France.

Gait Analysis Multi Organ Computed Tomography Segmentation Patient Trajectories Biomechanics Clustering

Aug 31, 2026cs.CV

Pretrained, Curriculum-Tuned, and Ensembled: A Tracer-Aware Interactive Segmentation Pipeline for AutoPET V

Interactive lesion segmentation in whole-body PET/CT requires a model to provide a strong initial prediction while also responding efficiently to sparse corrective scribbles during inference. This setting is particularly challenging because tracer distributions, physiological uptake patterns, lesion appearance, and acquisition characteristics differ substantially between FDG and PSMA studies. We present TRIAGE, Tracer-aware Refinement via Interactive Anatomy-Guided sEgmentation. The core backbone is a 3D STU-Net initialized through masked autoencoding pre-training with an asynchronous masking strategy, aiming to learn transferable anatomical and cross-modal representations before task-specific fine-tuning. In parallel, we train an auxiliary organ segmentation model whose predictions provide explicit anatomical context and help distinguish physiological uptake from malignant lesions. A dedicated tracer classifier first routes each study to an FDG- or PSMA-specific branch. Within each branch, a first-stage segmentation model consumes CT, PET, and organ context to generate an initial lesion mask. The initial prediction is then combined with cumulative foreground/background scribbles and refined by a second interactive segmentation network. The FDG and PSMA branches share the same overall processing pipeline but are trained independently to account for tracer-specific appearance and error modes. We additionally employ curriculum-style training and model ensembling to improve robustness across interaction steps and heterogeneous cohorts. Experiments are conducted using the official AutoPET V data and ten-fold split; quantitative results, ablations, and final test-set performance are left as placeholders to be completed after the challenge evaluation. Code: https://github.com/Liiiii2101/AUTOPET2026-MEDAI.

Xinglong Liang, Chunyao Lu, Tianyu Zhang +4

Department of Radiology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands · Department of Radiology and Nuclear Medicine, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands · Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao Special Administrative Region of China +2

Lesion Segmentation Multi Organ Computed Tomography Segmentation Pretraining Fedavg

Aug 31, 2026cs.CV

ImageCAS-X: a dataset and benchmark for coronary artery segmentation and centerline extraction in coronary CT angiography

Accurate segmentation of the coronary vessel lumen is a prerequisite for quantitative assessment of atherosclerotic plaque and perivascular adipose tissue in coronary computed tomography angiography (CCTA). Cardiologists rely on semi-automated methods for this task because manual vessel tracing and segmentation are labour-intensive. Although many automated methods have been proposed, their validation remains limited by the lack of large, high-quality publicly available datasets. We provide a new dataset of voxel-wise annotations of the vessel lumen and coronary segments, alongside centerlines, and mesh surfaces for 800 scans from the publicly available ImageCAS dataset. Using this dataset, we benchmark established lumen segmentation methods against inter-observer variability, stratifying performance by disease, image quality, coronary dominance, coronary segment, vessel diameter, and lumen attenuation. These labels allow segmentation accuracy to be described in anatomical and clinical context rather than reported as a single aggregate score. The dataset supports the development and validation of methods for lumen segmentation, plaque and perivascular quantification, and haemodynamic modelling.

Kit M. Bransby, Esther Øksnebjerg, Kristoffer Kjær +7

DTU Compute, Technical University of Denmark, Kongens Lyngby, Denmark · Cardiovascular Research Unit, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark

Coronary Angiography Multi Organ Computed Tomography Segmentation Vision Datasets Extraction

Aug 5, 2026cs.CV

Enhancing Low Back Pain Assessment with Diffusion Models for Lumbar Spine MRI Segmentation

This study introduces a diffusion-based framework for robust and accurate semantic segmentation of lumbar spine MRI scans from patients with low back pain (LBP), regardless of whether the scans are T1- or T2-weighted. We compared with advanced models for segmenting vertebrae, intervertebral discs (IVDs), and spinal canal using the SPIDER dataset. The results showed that SpineSegDiff achieved a segmentation performance comparable to that of the state-of-the-art non-diffusion nnUnet, particularly in improving the identification of degenerated IVDs. In addition, the uncertainty maps generated by our model provide valuable insights for clinical review, enhancing the robustness and reliability of the segmentation results. The potential of diffusion models to enhance the diagnosis and management of LBP through more precise analysis of pathological spine MRI is underscored by our findings.

Maria Monzon, Thomas Iff, Ender Konukoglu +1

Biomedical Data Science Lab, ETH Zürich, Zürich, Switzerland · Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland · Computer Vision Lab, ETH Zürich, Zürich, Switzerland

Multi Organ Computed Tomography Segmentation Diffusion Models

Aug 5, 2026cs.CV

Segmentation Pre-training for Label-Efficient Lumbar Spine Degeneration Grading

Automated assessment of degenerative pathology in the lumbar spine on magnetic resonance imaging (MRI) requires access to large-scale datasets of expert-annotated radiological gradings. In contrast, segmentation pseudo-labels can be generated by automated tools at negligible radiologist cost. We examine whether pre-training on segmentation can effectively replace a fraction of the manual grading annotations required for downstream supervision. We pre-train a 3D ResNet encoder to segment the vertebrae, intervertebral discs (IVDs), and the spinal canal, then fine-tune lightweight task-specific grading heads using different proportions of the available training data, ranging from

10\%

to

100\%

. On a multicentre dataset of

{\sim}2{,}000

subjects across 11 pathologies, segmentation pre-training, achieving a Dice score of

0.94

against pseudo-labels, improved the task-averaged (macro) one-vs-rest ROC-AUC at all proportions. With only 20% of grading labels after pre-training, the method achieved near full-supervision performance, with the largest gains observed for either low-prevalence or spatially grounded pathologies.

Monzon Maria, Zisserman Andrew, Jutzeler Catherine R. +1

Biomedical Data Science Lab, Dept. D-HEST, ETH Zurich, Zurich, Switzerland · Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland · Visual Geometry Group, Dept. of Engineering Science, University of Oxford, UK

Multi Organ Computed Tomography Segmentation High Confidence Pseudo-Labels

Aug 1, 2026cs.CV

Test-time Adaptation of Pelvic Bone Segmentation Models via Dynamic Reliability-Guided

Reliable pelvic bone segmentation (PBS) from CT is essential for robot-assisted pelvic trauma surgery, yet deploying a source-trained model to a new hospital suffers from severe performance degradation due to cross-center domain shifts. While test-time adaptation (TTA) enables online model adaptation without accessing source data, existing methods show limited effectiveness for PBS, facing challenges including boundary degradation, anatomical inconsistency under domain shifts, and voxel-level class imbalance. To address these challenges, we propose a novel closed-loop dynamic Reliability-Guided TTA framework (ReGA) for PBS. Specifically, we introduce a pseudo-label reliability criterion termed Segmentation Inference Consistency Evaluation (SICE), which jointly measures region overlap and boundary deviation via dropout-based ensemble predictions. Based on SICE, a trust-weighted refinement module adaptively updates features to mitigate boundary errors in pseudo-labels. Furthermore, a confidence-weighted region-level contrastive learning strategy is proposed to enforce anatomical consistency. Finally, ReGA follows the teacher-student (TS) scheme to alleviate voxel-level class imbalance. Experiments on three heterogeneous 3D pelvic CT datasets demonstrate that ReGA consistently outperforms state-of-the-art TTA methods, enabling effective adaptation of the source-trained PBS model to unseen clinical domains. The code is available at https://github.com/Ren-ling/ReGA.

Ling Ren, Chao Deng, Ziming Wang +2

College of Automation, Nanjing University of Posts and Telecommunications, Nanjing 210003, China · Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583 · State Key Laboratory Cultivation Base of Research, Prevention and Treatment for Oral Diseases, the Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing 210029, China

Multi Organ Computed Tomography Segmentation Test-Time Adaptation Mitigating Domain Shift Image Registration Anatomy

Jul 30, 2026cs.CV

AuricularWorld: Hierarchical Action-Guided World Modeling for Fine-Grained Auricular Structure Segmentation from CT Scans

Fine-grained segmentation of auricular structures in CT is challenging because the ear occupies a small image region, cartilage boundaries are highly irregular, and interfaces between cartilage and surrounding soft tissues are often ambiguous. Clinical annotations may also include both composite structures containing cartilage and adjacent skin and their corresponding cartilage-only regions, producing nested and overlapping labels. We propose a world-model-based segmentation framework that enables iterative anatomical reasoning beyond conventional feed-forward prediction. Built on an encoder-decoder architecture, the framework introduces a deterministic recurrent state-space model into the intermediate latent space. Multi-scale encoder features and partially decoded representations are fused to form a structural observation that initializes the latent dynamics. During inference, the model performs a three-step latent rollout without ground-truth guidance. Hierarchical anatomical actions update the recurrent state and progressively refine the latent representation. The resulting latent trajectory is projected back into the decoder and combined with high-resolution features to produce the final segmentation. To learn reliable latent transitions, we introduce a balanced hierarchical action objective that addresses foreground sparsity, missing anatomical groups, and imbalance between add and remove operations. Extensive experiments show that the proposed framework consistently improves segmentation accuracy and reduces HD95 by more than 43% for small, irregular, and overlapping auricular structures in CT. These results demonstrate the effectiveness of latent world-model reasoning for challenging medical image segmentation.

Jingwen Yang, Senmao Wang, Luoyao Kang +6

Plastic Surgery Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100144, China · The Chinese University of Hong Kong, Hong Kong SAR, 999077, China · The Chinese University of Hong Kong (Shenzhen), Shenzhen, 518172, China

Multi Organ Computed Tomography Segmentation Anatomy World Models Latent Space

Jul 30, 2026cs.CV

Same Branches, Different Trees: A Bifurcation Connectedness Metric for Coronary Artery Segmentation and FFR-CT Decision Agreement

Fractional flow reserve derived from CT angiography (FFR-CT) simulates flow through a patient-specific vessel model, so its accuracy depends on the connectedness of the segmented tree, not only on volumetric overlap: a segmentation can reach high Dice yet sever a bifurcation, dropping the downstream subtree and reversing the treatment decision. Topology-aware losses such as clDice and Skeleton Recall act on the global centreline and can miss localised breaks. We study the Bifurcation Connectedness Score (BCS), which scores connectedness at each ground-truth bifurcation, and soft-BCS, its differentiable training surrogate. BCS captures a property of segmentation quality the standard metrics miss: it responds strongly to breaks in connectedness while staying largely unchanged under connectedness-preserving narrowing. Higher BCS accompanies closer agreement between the FFR-CT decisions a solver makes on predicted versus ground-truth geometry, most clearly in severe disease (OR 2.16, CI [1.23, 4.18]). Both decisions come from the same solver, so this reflects geometric, not clinical, fidelity. In training, soft-BCS and Skeleton Recall recover the same branches but build different trees. Recovering branches and keeping them connected are separable properties, so we recommend reporting a measure of each.

Maame Owusu-Ansah, Kelvin Lee, Dr Vinod Venugopal +3

Applied Vision & Artificial Intelligence Lab, School of Engineering & Physical Sciences, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom · Lincolnshire Heart Centre, United Lincolnshire Teaching Hospitals Trust, Lincoln, United Kingdom · School of Computer Science & Informatics, De Montfort University, The Gateway, Leicester LE1 9BH, United Kingdom

Coronary Angiography Multi Organ Computed Tomography Segmentation Left-Ventricular Ejection Fraction Bifurcation Skeleton

Jul 28, 2026cs.CV

Open-Ended CT Volume Segmentation with Weak Supervision from Language

We introduce a method for training a text-conditioned segmentation model for CT scans, which combines voxel-level supervision with coarse but scalable slice-level supervision from reports. We extract, from a large database of scan-report pairs, descriptions of findings with indices of slices where those findings occur. We then finetune a general-purpose 2D image segmentation model, SAM3, with standard segmentation losses from strongly labeled data and with a slice-level classification loss from the extracted weak supervision. Our results on the ReXGroundingCT dataset illustrate that this strategy improves the segmentation dice score: from an 8% relative gain when there are 1000 fully labeled volumes to 22% when there are 250 fully labeled volumes.

Sanjay Subramanian, Junwei Yu, Zirui Wang +5

Department of Electrical Engineering and Computer Science, UC Berkeley · Voio · Department of Radiology and Biomedical Imaging, UC San Francisco +1

Multi Organ Computed Tomography Segmentation Voxel Volume Loss Function

Jul 22, 2026cs.CV

PhenSPINE: A Standardized Benchmark for Spine Pathology Diagnosis

The accurate diagnosis of spinal pathologies depends heavily on radiological interpretation, yet automated systems are hindered by the lack of diverse, high-quality benchmarks. In this study, we present PhenSPINE, a Magnetic Resonance Imaging dataset comprising 16,813 images from 250 patients, curated to facilitate advanced deep learning research. We propose a robust diagnostic benchmark that integrates state-of-theart convolutional backbones with a Positional Encoding mechanism to explicitly model the anatomical context of intervertebral discs. Evaluating across four standard MRI sequences, our experiments demonstrate that the Sagittal T2-weighted sequence offers the most robust diagnostic value, achieving a superior Macro F1-score of 50.31%. We find that multisequence fusion strategies yield inferior performance compared to this single-sequence baseline, as the images across sequences in our dataset are significantly compromised by noise interference from surrounding anatomical regions. This work establishes a robust baseline and offers critical insights into sequence selection for spine analysis.

Duong Ngoc Vu, Hai Son Nguyen, Trong-Nghia Nguyen +4

Business AI Lab, College of Technology, National Economics University, Vietnam · Medical Imaging & Radiological Technology Department, Faculty of Medical Technology, Phenikaa School of Medicine & Pharmacy, Phenikaa University, Vietnam · Radiology and Functional Exploration Center, Phenikaa University Hospital, Vietnam +1

Magnetic Resonance Imaging Dataset Multi Organ Computed Tomography Segmentation Diagnostic Benchmark Diagnosis

Jul 18, 2026cs.CV

Automated Cardiac Adipose Tissue Segmentation in Computed Tomography: A Literature Review

This review provides an overview of recent advancements in automated segmentation methods on Computed Tomography (CT) for two types of cardiac fat: Epicardial adipose Tissue (EAT) and Pericardial Adipose Tissue (PAT). These fat deposits, separated by the pericardium, have been linked to various cardiovascular diseases, with EAT receiving the most research attention. Their complex anatomical context makes manual quantification highly time-consuming and prone to considerable inter-observer variability. Automated methods effectively address these complications, offering a more efficient and consistent solution. This study encompasses a broad range of methods, spanning AI as well as non-AI approaches. Additionally, it presents the remaining challenges, including the need for larger annotated public datasets and optimized attenuation thresholds for contrast-enhanced CT. It is demonstrated that automated methods are able to achieve segmentation results comparable to the quality of human annotation, proving their potential as a clinical tool for discovering new biomarkers and enhancing patient outcomes.

Andreas W. Aspe, Jonas Jalili Pedersen, Andreas Ohrt Johansen +4

DTU Compute, Technical University of Denmark, Kongens Lyngby, Denmark · Heart Centre, Rigshospitalet, Copenhagen, Denmark, Denmark · Novo Nordisk A/S, Søborg, Denmark

Echocardiography Multi Organ Computed Tomography Segmentation Cone-Beam Computed Tomography Human Annotations Review Literature Review

Jul 17, 2026cs.CV

Spatial Normalization for Cross-Domain Retinal Layer Segmentation in Optical Coherence Tomography

Retinal layer segmentation in Optical Coherence Tomography (OCT) is a fundamental step for extracting quantitative biomarkers of retinal structure. Indeed, there is a growing interest in the analysis of OCTs in the context of neurodegenerative diseases. However, segmentation remains challenging due to speckle noise, shadowing artifacts, low contrast between adjacent layers, anatomical variability across subjects, and domain shifts arising from different acquisition protocols and clinical populations. While deep learning methods have achieved remarkable performance, their robustness and generalization across heterogeneous datasets remain limited. In this work, we investigate the role of spatial normalization as a preprocessing strategy to mitigate geometric domain shifts and improve the consistency of retinal layer segmentation. Inspired by standard practices in neuroimaging, we introduce a fovea-centered normalization framework that aligns OCT volumes into a common anatomical reference. We perform a comprehensive evaluation of state-of-the-art deep learning architectures. To provide a comprehensive assessment of segmentation quality, we combine conventional overlap-based metrics at B-scan level with topology-aware metrics at A-scan level and thickness-based measures at the en-face level. In cases where a ground truth is not available, we propose topology violation quantitative metrics that do not require ground truth annotations and a thickness-based qualitative assessment that captures structural consistency and clinically relevant patterns at the en-face level. The results demonstrate the importance of spatial normalization in OCT segmentation pipelines toward the development of robust and clinically meaningful retinal analysis tools, enabling reliable biomarker extraction and downstream computational analysis in neurodegenerative research.

Iker Moran-Cavero, Monica Hernandez, Elvira Mayordomo +4

Optical Coherence Tomography Vessel Segmentation Multi Organ Computed Tomography Segmentation

Jul 13, 2026cs.CV

A Unified Framework for Comprehensive Cardiac CT Segmentation and Phenotyping: Human-in-the-Loop Data Annotation, Vision Foundation Model Development, Multicenter Evaluation and Clinical Validation

Comprehensive quantification of cardiac structures from computed tomography (CT) remains limited not by data availability but by the scalability of measurements, which makes routine use impractical. Here we present a unified framework for comprehensive cardiac CT segmentation and phenotyping that combines a human-in-the-loop annotation pipeline, a cardiac CT augmentation technique, and a self-supervised foundation model pre-trained on 60,000 unlabeled cardiac CT scans. Using this approach, we assembled the largest and most comprehensive expert-annotated cardiac CT segmentation dataset to date, comprising 1598 cases and 14 distinct cardiac structures (1000 for training, 598 for the external test set). Across five external datasets, the framework segmented all structures more accurately and comprehensively than existing open-source tools. Self-supervised pre-training improved labeling efficiency, with the most significant gains observed during external evaluation in the low-data regime. Benchmarking across convolutional, transformer, and state-space architectures showed comparable performance, indicating that data quality and pre-training, rather than architecture, drove accuracy. The framework was scaled to population-level phenotyping, with segmented anatomy that carries functionally relevant information about ventricular function and disease severity beyond demographic variables. By openly releasing the largest dataset with human labels, code, model weights, a CT augmentation library, and software, this work provides a reproducible foundation for opportunistic cardiac phenotyping from routinely acquired CT scans.

Pooya Mohammadi Kazaj, Leo Fridolin Weber, Wen Xie +17

Department of Cardiology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland · Department of Digital Medicine, University of Bern, Bern, Switzerland · Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland +4

Echocardiography Multi Organ Computed Tomography Segmentation Cone-Beam Computed Tomography Phenotypes Multicenter Evaluation

Jul 8, 2026eess.IV

False Confidence: Automated Labels Confound Fairness Audits in Cervical Spine Segmentation

Automated segmentation of cervical-spine MRI is increasingly used in clinical workflows, yet no fairness audit exists for this anatomy. We show that auditing these segmentation tasks is complicated by a common property of modern segmentation datasets: expert-annotated gold labels are expensive, so abundant machine-generated (silver) labels are added to limit annotation cost. This matters because the reference used to judge a model can itself be biased. In this study, we present the first fairness audit of cervical-spine MRI segmentation across sex, age, and race using the CSpineSeg dataset. We observe that the deployed model is demographically fair, but the choice of reference label, however, is not neutral. Because a dataset's silver labels are generated by a model trained on its gold labels, any new model trained on those same gold labels agrees more with the silver labels than with expert truth: scoring identical predictions against silver rather than gold overestimates performance by ~8 Dice points and turns the fairness verdict for age from non-significant to significant - not by the gap inflation Parikh et al. report (which we term false magnitude) but by collapsing within-group variance (which we term false confidence). Reference-label provenance is thus a first-order confounder in segmentation evaluation: performance and fairness should be reported against expert labels, and any fairness claim stated together with the provenance of its reference.

Linus Juni, Aasa Feragen, Aditya Parikh

Section for Visual Computing, DTU Compute, Technical University of Denmark, Kongens Lyngby, Denmark

Multi Organ Computed Tomography Segmentation Fairness Audits Algorithmic Fairness Provenance

Jul 8, 2026eess.IV

Towards Accurate and Fast Clinical Body Composition: A Resource-Efficient Hierarchical Segmentation Framework for Multi-Source CT

Background: Automated 3D segmentation of muscles and adipose tissue from CT is vital for body composition analysis, but multi-source data heterogeneity and high CPU memory demands hinder clinical deployment. Methods: We propose a coarse-to-fine hierarchical framework to segment ten tissue structures. Efficiency is optimized using Dynamic Spacing and Anisotropic Patching, a Group Inference mechanism for low-memory sliding-window processing, and Topology-Aware Asymmetric Resampling for fast post-processing. Results: The framework was trained on 1,558 CT volumes from seven public and two private datasets, and evaluated on an independent test cohort (N=105), per-structure Dice coefficients ranged from 0.924 to 0.982. Eight major structures met the +-10% relative error clinical acceptance limit. On a 12-core CPU workstation, the GPU-free pipeline averaged 44.5 seconds per volume with 4.73 GB peak memory. Conclusion: This framework balances accuracy and efficiency, enabling robust, large-scale body composition analysis on standard CPU workstations.

Xiaodi Shen, Qingzhu Zheng, Yaoyang Qiu +12

Department of Radiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China · Research & Development Center, Canon Medical Systems (China) Co. Ltd. Beijing 100015, China

Multi Organ Computed Tomography Segmentation Cone-Beam Computed Tomography Tissue Body Resampling

Jul 6, 2026cs.CV

Be Indiscrete: The Benefits of Learning Continuous Spine Degeneration Severity Scores

Lumbar spine degeneration is a major contributor to chronic low back pain and is routinely assessed on MRI using ordinal grading systems, e.g. normal, mild, moderate, severe. Consequently, most approaches to train models to grade these MRIs formulate grading as a multi-class classification problem, treating ordinal grades as categorical, ignoring differences in misclassification severity, and imposing hard decision boundaries on a continuous disease process. This work explores modeling spinal degeneration as a continuous severity ranking problem. We introduce SpineRankNet, a framework that learns scalar severity scores from lumbar spinal MRI, and compare it against multi-class classification and ordinal regression. Using multiple degeneration measures from the Genodisc dataset, we show that a model trained using a ranking loss to produce a continuous score enables fine-grained ordering of MRI scans. Furthermore, the ordinal grading classes can be recovered from the score with comparable accuracy to those from a model trained directly for classification. The score learned by ranking even improves discrimination between more distant classes. Source code is available at https://github.com/spinetools/spineranknet.

Maria Monzon, Andrew Zisserman, Robin Y. Park +2

Biomedical Data Science Lab, Dept. D-HEST, ETH Zurich, Zurich, Switzerland · Swiss Institute of Bioinformatics (SIB), Lausanne, 1015, Switzerland · Visual Geometry Group, Dept. of Engineering Science, University of Oxford, UK

Severity Multi Organ Computed Tomography Segmentation Magnetic Resonance Imaging

Jul 2, 2026eess.IV

Population-Scale Segmentation of Penile Tissue in DIXON MRI using Deep Learning for Quantitative Phenotyping in Male Reproductive Health

Penile measurement is clinically relevant across male reproductive and urogenital health, including conditions such as micropenis, congenital and endocrine disorders, and sexual or urinary dysfunction. However, quantitative assessment of penile size has relied mainly on external length or circumference measurements, which are difficult to standardize, sensitive to measurement conditions, and unable to capture the internal portion of the penis. MRI enables volumetric assessment of the whole penis in vivo, but automated segmentation has not previously been established at population scale. Automated whole-organ volumetry would enable high-throughput phenotyping for multi-omics and clinical studies of male reproductive disease. Here, we present a deep learning framework for whole-penis segmentation in multi-channel DIXON MRI. Using a newly curated expert-annotated training dataset (

n = 145

subjects;

13,050

annotated slices) and a double-annotated independent test benchmark (

n = 24

subjects;

2,160

double-annotated slices), we optimized a 3D nnU-Net architecture. The model achieved a 5-fold cross-validation Dice score of

0.90

and performed at observer-level accuracy on the independent test set (Dice:

0.92

; Hausdorff distance:

3.58

). We deployed the model in

34,412

UK Biobank participants, enabling automated quantification of total penile tissue, including both external and internal components. Longitudinal evaluation in 2,282 men demonstrated high inter-session reproducibility (

r = 0.87

). This framework establishes a reproducible and population-scalable method for MRI-based assessment of penile anatomy and provides an open technical resource for future studies in urological imaging and male reproductive health. The trained model weights will be publicly released.

Jan Ernsting, Gunnar Paul Kordes, Nils Johannaber +5

University of Münster Germany

Prostate Magnetic Resonance Imaging Multi Organ Computed Tomography Segmentation Magnetic Resonance Imaging Morphometric Analysis Phenotypes Volume+1

Jun 30, 2026cs.CV

Temporal Training Strategies for Left Atrium and Left Atrial Appendage Segmentation in Dynamic Contrast 4DCT

Dynamic contrast-enhanced cardiac CT enables time-resolved analysis of contrast filling and washout in the left atrium (LA) and left atrial appendage (LAA), with potential applications for assessing blood stasis in atrial fibrillation (AF). Accurate segmentation across all frames is required for such analysis but is challenging due to large temporal contrast variations and the use of a single annotation per registered sequence. This creates a trade-off between training for robustness and limiting label noise. In this study, we investigate how temporal training-set design affects nnUNet-based segmentation of the LA and LAA in dynamic 4DCT. We compare training using a minimal two-frame dataset reflecting standard clinical practice, a physiologically selected subset of frames, and the full 27-frame sequence. We further evaluate the impact of foreground-based normalization. Training with all frames yielded the best performance in early low-contrast phases. However, the physiologically selected subset achieved comparable performance from the filling phase onward. Applying normalization parameters derived from the full dataset improved performance of reduced datasets in low-contrast frames, but did not fully close the gap. These findings highlight the importance of temporal diversity in training data for robust segmentation in dynamic CT, while indicating that carefully selected frame subsets may provide an effective trade-off between performance and efficiency for downstream applications.

David Montalvo-García, Lauren Severance, Elliot R. McVeigh +1

Biomedical Image Technologies, ETSI Telecomunicación, Universidad Politécnica de Madrid, Madrid, Spain · Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain · Department of Bioengineering, University of California San Diego, La Jolla, CA, USA +2

Echocardiography Multi Organ Computed Tomography Segmentation Normalization

Jun 29, 2026cs.CV

From Raw Segmentations to Simulation-Ready Cardiac Meshes: An Automated Framework for Anatomical Reconstruction and Virtual Cohort Generation

Computational models of the human heart are widely used to study electromechanical and fluid-dynamical cardiac function and to support applications such as in silico clinical trials. However, most studies remain limited to single or patient-specific anatomies, restricting the inclusion of population-level variability required for uncertainty quantification. A key challenge is translating medical-image segmentations, which may contain artifacts, mesh defects or disjoint domains, into topologically coherent geometries suitable for multiphysics simulations. In this work, we present a semi-automatic pipeline that converts CT-based segmentations into simulation-ready cardiac meshes within a few minutes while preserving anatomical and topological consistency. Building on modern deep learning segmentation methods, the framework incorporates a template-based registration stage to regularize artifacts and enforce mesh-quality constraints. A Chamfer-distance morphing strategy deforms a high-quality template toward each segmented heart, matching individual chambers while preserving topology. The resulting meshes are watertight, isotopological, and endowed with consistent point-to-point correspondence. The pipeline is validated on 58 healthy cardiac CT scans, including all cardiac chambers and proximal vessel segments. The resulting meshes can be represented in a unified shape space, enabling the construction of a statistical shape model of the heart and major vessels. Principal Component Analysis shows that a low-dimensional latent space efficiently captures population variability, while Gaussian Mixture Modeling enables synthetic anatomy generation. Overall, the proposed framework (released open-source) provides a pathway from raw segmentations to simulation-ready cardiac geometries, enabling anatomically consistent virtual cohorts for large-scale in silico studies.

Francesco Fabbri, Martino Andrea Scarpolini, Paolo Ciancarella +4

Gran Sasso Science Institute (GSSI), L’Aquila, Italy. · European Hospital, Rome, Italy. · University of Edinburgh, Edinburgh, Scotland. +2

End-To-End 4D Heart Mesh Recovery Across Full-Stack Multi Organ Computed Tomography Segmentation Anatomy Statistical Shape Model Cohort

Jun 22, 2026eess.IV

Promise and challenges of heart chamber segmentation from non-contrast CT scans using contrastive unpaired image translation: a feasibility study

Purpose: To evaluate the feasibility and challenges of heart chamber segmentation from non-contrast CT scans using contrastive unpaired image translation and deep learning-based segmentation. Approach: We developed ChameleonNet, a framework utilizing the Contrastive Unpaired Translation (CUT) network with decoupled contrastive learning (DCL) loss to synthesize non-contrast CT from contrast CT scans. Using annotations of four heart chambers (left atrium (LA), left ventricle (LV), right atrium (RA), and right ventricle (RV)) from contrast scans, we trained a Hausdorff distance loss-enhanced nnU-Net on synthesized non-contrast images. The translation model was trained with 35,538 contrast-enhanced and 37,197 non-contrast CT slices. The segmentation model was trained with 292 synthesized non-contrast scans. Performance was evaluated using Dice similarity coefficient (DSC) and 95th Hausdorff distance (HD95) on 36 synthesized non-contrast scans, and volume agreement on 36 real non-contrast CT scans was assessed using Pearson correlation, mean absolute percentage error (MAPE), and mean percentage error (MPE). Results: The segmentation model achieved DSC of 0.94 (0.01), 0.91 (0.04), 0.92 (0.03), 0.93 (0.02), and HD95 of 3.63 (1.49), 5.74 (4.08), 5.18 (1.77), 5.51 (3.21) mm on synthesized non-contrast images for LA, LV, RA, and RV, respectively. On real non-contrast CT scans, Pearson correlations were 0.93, 0.82, 0.87, and 0.89 (all p<0.001), with MAPE ranging from 9.22% to 20.79%, and MPE ranging from -12.52% to 4.67%. Conclusions: ChameleonNet demonstrated feasibility for heart chamber segmentation from non-contrast CT without manual non-contrast annotations. However, volume errors, particularly for LV and RV, indicate that further refinement and validation are needed before clinical use.

Jing Wang, Tong Yu, Hao-En Lu +5

Department of Radiology, University of Pittsburgh, Pittsburgh, PA 15213, USA · Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA · Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA

Echocardiography Multi Organ Computed Tomography Segmentation Unpaired Image-To-Image Translation Contrast Challenges

Jun 20, 2026cs.CV

Accurate identification and measurement of the precipitate area by two-stage deep neural networks in novel chromium-based alloys

The performance of advanced materials for extreme environments is underpinned by their microstructure, including the size and distribution of reinforcing phases. Chromium-based superalloys are a recently proposed alternative to conventional face-centred-cubic superalloys for high-temperature applications, such as Concentrated Solar Power, and their development requires efficient measurement of precipitate volume fraction and size distribution from electron microscopy images. Traditional fixed-threshold image processing is sensitive to background noise, generalises poorly across materials, and requires substantial manual measurement effort. To address these bottlenecks, this study proposes DT-SegNet, an end-to-end two-stage deep learning scheme based on YOLOv5 and SegFormer for object detection and segmentation in electron microscopy images. The approach combines the training efficiency of convolutional neural networks at the detection stage with the segmentation accuracy of a Vision Transformer. Numerical experiments show that DT-SegNet substantially outperforms state-of-the-art segmentation tools offered by Weka and ilastik across metrics including accuracy, precision, recall, and F1-score. The model provides a useful tool for alloy-development microstructure examinations and helps address the large datasets associated with high-throughput alloy development.

Zeyu Xia, Kan Ma, Sibo Cheng +7

Queensland University of Technology, Queensland 4000, Australia · School of Metallurgy and Materials, University of Birmingham, Birmingham B15 2SQ, United Kingdom. · Data Science Institute, Department of Computing, Imperial College London, London SW7 2AZ, United Kingdom. +4

Shape-Memory Alloy Porous Media Multi Organ Computed Tomography Segmentation Object Detection Neural Network Rainfall

Jun 19, 2026eess.IV

Scaling up fine-grained intracranial vessel annotations in computed tomography angiography

In this work, we present SemanticVessel, a dataset for fine-grained brain vessel segmentation in computed tomography angiography scans. Based on the detailed contrast provided by dynamic 4D-CTA scans, we generate segmentation traces for arteries and veins. We then use intensity-guided region growing to obtain segmentations of the majority of vascular territories in the human brain, which are refined and annotated with 20 unique arterial classes by an expert radiologist. Unlike existing datasets, where minor arteries are discarded as background content, we merge these minor arteries into a generic arterial class. Due to the multiple-phase acquisition of dynamic 4D-CTA, labels for a single phase can be re-used for other phases in the same series, greatly increasing the size of our dataset with no additional annotation cost. The results show that models trained with the additional generic artery class produce better fine-grained segmentations across the board. We will make our code, annotation GUI, and model weights available to the scientific community. Code, weights, and data will be made available on https://github.com/alceballosa/robust-vessel-segmentation

Chu-Hsuan Lin, Alberto Mario Ceballos-Arroyo, Jisoo Kim +4

Brigham and Women’s Hospital, Harvard Medical School Boston, MA, USA · Khoury College of Computer Sciences, Northeastern University Boston, MA, USA · Washington University in St. Louis St. Louis, MI, USA +1

Vessel Segmentation Coronary Angiography Multi Organ Computed Tomography Segmentation 4D Generation

Jun 19, 2026eess.IV

Anatomically Consistent TMJ Disc Segmentation via Semantic Anchoring and Clinical Priors

Segmenting the temporomandibular joint (TMJ) disc from MRI is essential for accurate diagnosis of internal derangement, yet it remains unreliable in practice due to its small size, low contrast, and morphological variability. Existing methods, primarily adapted from general segmentation architectures, often produce fragmented or anatomically inconsistent masks, leading to unstable measurements of disc position and shape for downstream diagnosis. To address these challenges, we propose TISC, a TMJ disc segmentation framework that integrates semantic anchoring with clinical metadata-guided boundary refinement. The framework first establishes robust disc localization in the foundation model feature space via a Prototypical Semantic Anchoring (PSA) module that aggregates adjacent-slice MedDINOv3 features and derives a prototype-driven similarity map. It then performs targeted boundary refinement through a Clinical-Metadata Point Refinement (C-MPR) module, with point-wise predictions modulated by Mouth Open Limitation (MOL), a clinical indicator associated with disc displacement without reduction. On a large-scale cohort of 2,488 PD MRI volumes from 1,300 patients, our method achieves up to a 4.96 Dice improvement over strong baselines across diverse architectures, delivering more anatomically coherent and clinically reliable TMJ disc segmentation.

Dayun Ju, Chanyoung Kim, Sunyoung Jung +4

Department of Artificial Intelligence, Yonsei University, Seoul, Republic of Korea · Department of Computer Science, Emory University, Atlanta, Georgia, USA · College of Dentistry, Yonsei University, Seoul, Republic of Korea

Multi Organ Computed Tomography Segmentation Magnetic Resonance Imaging Occlusal Constraint Semantic Anchor Slices Prior Knowledge Integration

Jun 17, 2026cs.CV

GUMP-Net: An interpretable model-data-driven intelligent algorithm for multi-class pelvic segmentation

Pelvic segmentation is one of the most important and fundamental research problems in precise and intelligent diagnosis and treatment, as well as surgical planning and navigation for pelvic fractures. By combining an improved geodesic active contour model with deep neural networks, we propose GUMP-Net, an interpretable model-data-driven intelligent algorithm for multi-class pelvic segmentation, in which three network modules are designed to constitute the overall segmentation framework together: the object detection module for automatic level set initialization, the edge detector module for learning an anatomy-aware edge detector function and the iteration module for deep level set evolution. Leveraging the advantages of level set representation and deep learning, GUMP-Net shows more accurate, robust and consistent segmentation performance, especially in small training data situation, compared to the state-of-the-art methods. Extensive experiments on pelvic datasets demonstrate the rationality and effectiveness of the proposed algorithm. Further experiments extended to ankle dataset indicate broader applications to other anatomies. The proposed algorithm not only provides an efficient segmentation method for complex fracture reduction, but also gives an interpretable geometric perspective for understanding deep learning segmentation.

Liheng Wang, Yinghui Zhang, Licheng Zhang +3

State Key Laboratory of Mathematical Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100190, China. · University of Chinese Academy of Sciences, Beijing 100190, China. · State Key Laboratory of Mathematical Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China. +4

Multi Organ Computed Tomography Segmentation Edge

Jun 14, 2026cs.CV

CPS4: Class Prompt driven Semi-Supervised Spine Segmentation with Class-specific Consistency Constraint

Vision Language Model (VLM) has great potential to enhance the quality of pseudo labels in semi-supervised spine segmentation by leveraging textual class prompts to generate segmentation map, but no one has studied it yet. Although promising, it lacks explicit constraints to ensure consistency between spine class prompts and spine unit region, resulting in unsatisfactory performance in multi-class segmentation map generation. In this paper, we propose CPS4, the first text-guided semi-supervised spine segmentation network using class prompts to enhance the quality of spine pseudo labels. Specifically, CPS4 is implemented through two training stages. (i) Class-specific consistency constrained VLM pretraining stage: we propose token- and pixel-level attention loss to optimize the consistency between class prompts and spine units, forcing the textual class prompt to be closely coupled with the target spine unit in the semantic space. (ii) Class Prompt driven semi-supervised spine segmentation stage: using the pretrained vision-text encoder, we derive each class-specific binary segmentation map for the unlabeled spine image and integrate them into an unified multi-class segmentation map, improving the quality of the spine pseudo label generated by the semi-supervised spine segmentation network. Experimental results show that our CPS4 achieves superior spine segmentation performance with Dice of 80.44%, only using 5% labeled data on the public spine segmentation dataset, surpassing popular semi-supervised learning and VLM methods. Our code will be available.

Qingtao Pan, Hongzan Sun, Bing Ji +1

School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China · Department of Computer and Data Science, Case Western Reserve University, Cleveland, OH 44106, USA · Department of Nuclear Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China +1

Multi Organ Computed Tomography Segmentation High Confidence Pseudo-Labels Multiple Prompt Learning Frameworks Vision-Language Foundation Models Prompt Engineering

Jun 9, 2026cs.CV

IPSM-Bench: A New Intermediate Phase Segmentation Benchmark in Microstructure Images of Zinc-Based Absorbable Biomaterials

Zinc-based alloys are indispensable emerging absorbable metallic biomaterials, and their macroscopic performance is governed by microstructural characteristics. Intermediate phases-key microstructural constituents-are pivotal in regulating mechanical and functional properties. However, intermediate phase segmentation in zinc alloy microstructures faces formidable challenges: scarce annotated datasets, low contrast, difficulty detecting small targets, and heterogeneous morphologies. To this end, we construct IPSM-Bench, the largest high-quality dataset for zinc-alloy intermediate phase segmentation. Furthermore, we propose SCoP-SAM, a new Spatial Context Prior-guided SAM method that leverages the gradient structure and grayscale properties of intermediate phases to capture spatial context priors and incorporates them into the entire SAM encoding-decoding process, improving segmentation performance. Based on the proposed IPSM-Bench, we establish a new benchmark for intermediate phase segmentation to systematically evaluate state-of-the-art (SOTA) methods and advance research on zinc alloy microstructure analysis. Extensive experiments on IPSM-Bench and additional public alloy benchmarks demonstrate that our SCoP-SAM not only achieves SOTA performance for zinc-alloy intermediate phase segmentation but also generalizes remarkably well to other alloy scenarios.

Jinglin Xu, Shangyan Zhao, Jiabo Wang +5

School of Artificial Intelligence, University of Science and Technology Beijing, China · School of Materials Science and Engineering, University of Science and Technology Beijing, China · School of Big Data and Software Engineering, Chongqing University, China +3

Porous Media Multi Organ Computed Tomography Segmentation

Jun 8, 2026cs.CV

SpineReport: Automated 3D Quantification and Reporting of Lumbar Spine Degeneration on MRI

Lumbar spine conditions are a leading cause of disability worldwide, yet reliable quantification of degeneration from MRI remains challenging. In clinical practice, analysis is predominantly performed in two dimensions (2D), as manual three-dimensional (3D) assessment is time-consuming. However, 2D measurements suffer from limited reproducibility, particularly when anatomical structures are not aligned with the imaging plane. Existing automated approaches are often restricted to 2D, rely on discrete grading, or lack robustness and interpretability. We introduce SpineReport, an open-source, fully automated framework for comprehensive 3D morphometric analysis of lumbar spine MRI. Leveraging robust anatomical segmentations, the method extracts quantitative metrics from key structures, including the spinal canal, spinal cord, vertebrae, intervertebral discs, and foramina. These include both morphological and signal-based features, enabling cross-subject and longitudinal assessment. SpineReport further generates subject-specific reports that allow comparison with cohort distributions, improving interpretability and objective characterization of spinal morphology. Clinical relevance was evaluated against radiologist-reported severity grades for central canal, lateral recess, and foraminal stenosis. Metrics showed strong associations with central canal stenosis severity, with T2-weighted CSF signal providing the highest performance (AUC = 0.95). Canal AP diameter and area ratios also demonstrated strong correlations and high discriminative ability (AUC > 0.80). For lateral recess stenosis, associations were moderate, with lateral CSF signal being the most informative (AUC = 0.73). No significant associations were observed for foraminal stenosis despite robust region-of-interest extraction. SpineReport is released as an open-access tool: https://ivadomed.github.io/SpineReport/

Nathan Molinier, Adrian A. Marth, Reto Sutter +6

1NeuroPoly, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada · 2Mila, Quebec AI Institute, Montreal, QC, Canada · Department of Radiology, Balgrist University Hospital, Zurich, Switzerland +7

Morphometric Analysis Multi Organ Computed Tomography Segmentation Magnetic Resonance Imaging Degradation

Jun 8, 2026cs.CV

vesselFM-CT: Segmenting All Blood Vessels in CT Images for System-Level Cardiovascular Analysis

The vascular network in the human body is characterized by blood vessels exhibiting drastic structural variations in radius, length, topological properties, and branching patterns. This heterogeneity, together with location-specific anatomical background variations, poses a significant challenge for robust, large-scale analysis of the entire cardiovascular system. As a result, most research has focused on narrow, isolated segments of the vascular network. While such targeted studies provide valuable insights, they inherently limit the ability to assess the systemic health and functional integrity of the vascular network as a whole. In this work, we aim to bridge this gap to advance both clinical diagnostics and our fundamental understanding of vascular physiology. We propose the task of segmenting all vessels in CT images, ranging from the largest components of the cardiovascular system to even minuscule mesenteric vessels. To this end, we introduce vesselFM-CT, the first model capable of robustly segmenting all blood vessels in 3D CT images. VesselFM-CT is trained via an iterative, multi-step process and optimizes our proposed TubeLoss loss function, effectively addressing the inherent heterogeneity of the cardiovascular system. We demonstrate that vesselFM-CT outperforms all baselines and enables automated, precise extraction of the cardiovascular system from CT images, thereby unlocking a wide range of clinical and technical perspectives, including automated disease classification and synthetic CT image generation.

Bastian Wittmann, Chinmay Prabhakar, Suprosanna Shit +1

Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland

Vessel Segmentation Multi Organ Computed Tomography Segmentation Cone-Beam Computed Tomography Cardiac Vessels Anatomy+1

Jun 5, 2026eess.IV

Multi-planar 2D-U-Net Segmentation of 3D-CT Abdominal Organs augmented by Spatial Occurrence Maps

This work proposes a lightweight 2D-U-Net-based framework for segmenting five abdominal organs in large field-of-view 3D CT scans. The method combines coarse-to-fine segmentation, predictions from multiple anatomical planes, and additional fuzzy 3D spatial maps that provide anatomical location cues to improve segmentation accuracy. We combine multi-planar 2D-U-Net models augmented by a spatial occurrence map. The approach involves two main stages. First, the abdominal volume of interest region is detected by traversing the whole scan axially with a 2D-U-Net and determining the x-y-z-minimum and -maximum extents of the 5 abdominal organs of interest. Second, we use spatial occurrence maps to enhance our multi-planar 2D-U-net architecture inside the bounds from the former stage. The method is evaluated on 80 CT scans from various public sources. The results show Dice improvements of about 4% at maximum compared to the same model trained without spatial occurrence maps.

Daria Kern, Negar Chabi, Souraj Adhikary +1

Glasgow Caledonian University School of Science & Engineering Glasgow G4 0BA, United Kingdom · Jade University of Applied Sciences Department of Engineering & Medical Technology Germany, 26389, Wilhelmshaven, Germany

Multi Organ Computed Tomography Segmentation Cone-Beam Computed Tomography U-Net

Jun 4, 2026cs.CV

SC-MFJ: A Simple Haptic Quality Metric for Medical Image Segmentation

Standard segmentation metrics such as Dice and Hausdorff distance measure geometric overlap but say nothing about whether a segmented surface is suitable for haptic rendering in surgical simulation. We propose SC-MFJ (Surface-Constrained Mean Force Jerk), a simple, inexpensive metric that samples a segmented organ surface with many short virtual stylus walks and measures how jerky the resulting contact forces are. The metric is computed from existing segmentation outputs and uses roughly one minute of CPU time per case. We evaluate three pancreas CT segmentation approaches-binary nnU-Net output, Gaussian-smoothed output, and learned signed distance function (SDF) regression-across 80 cases in five-fold cross-validation. SC-MFJ reveals a 147x gap in haptic quality between the raw binary baseline and simple Gaussian post-processing, a difference entirely invisible to Dice and HD95. It also shows that learned SDF regression, despite requiring full model retraining, produces more variable haptic quality than Gaussian smoothing, with a case-level standard deviation of 168 N/s2 compared with 22 N/s2 for Gaussian. A second evaluation on the LiTS liver dataset (131 cases) confirms the generality of these findings: the binary-to-Gaussian gap widens to 189x, and Gaussian smoothing again produces consistently low force jerk across all folds. Our results suggest that for haptic simulation applications, a one-line post-processing step may be sufficient, and that a cheap metric like SC-MFJ can flag problems that geometric metrics miss.

Souraj Adhikary, Negar Chabi, Andre Mastmeyer

Jade University of Applied Sciences Friedrich-Paffrath-Str. 101 26389 Wilhelmshaven, Germany

Multi Organ Computed Tomography Segmentation Haptic Feedback Surgery Continuous Distance Field Force

May 30, 2026cs.CV

Pre-Deployment Robustness Stress Testing for CT Segmentation Systems Using Clinically Motivated Multi-Corruption Augmentation

Deep learning-based CT segmentation systems often achieve high accuracy on clean benchmark images, but their performance may degrade under heterogeneous clinical imaging conditions such as noise, resolution loss, contrast variation, intensity shift, and artifacts. This instability can limit reliable deployment in real-world medical imaging workflows. We propose Robustness via Augmented Multi-corruption Pipeline (RAMP), a robustness-oriented augmentation framework for CT segmentation. RAMP combines anatomically constrained spatial perturbations, CT intensity transformations, and stochastic multi-corruption composition to expose models to clinically plausible image degradation during training. Across two CT segmentation evaluation settings, RAMP achieved the strongest corrupted-image performance and the smallest clean-to-corrupted robustness gap. In the five-organ noisy evaluation benchmark, RAMP improved mean corrupted Dice from 0.610 to 0.753 and reduced the robustness gap from 0.264 to 0.064 compared with the nnU-Net baseline. In Abdomen1K, RAMP improved mean corrupted Dice from 0.633 to 0.789 and reduced the robustness gap from 0.290 to 0.070. Although RAMP did not achieve the highest clean-image Dice, it substantially mitigated worst-case segmentation collapse under severe image degradation. These results suggest that multi-corruption augmentation can serve as a practical pre-deployment strategy for improving the reliability of CT segmentation systems in heterogeneous clinical environments.

CholMin Kanga, Jonghyun Chung, Amanpreet Kaur +2

Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, Korea · Google Inc., 1600 Amphitheatre Parkway, Mountain View, 94043, California, United States

Multi Organ Computed Tomography Segmentation Stress Testing Evaluation Benchmarks

May 29, 2026cs.CV

LegSegNet: A Public Deep Learning System for Lower Extremity CT Tissue Segmentation and Quantification

Lower extremity computed tomography (CT) contains clinically relevant information for body composition analysis, sarcopenia assessment, and musculoskeletal disease monitoring, but extracting these measurements at scale requires accurate tissue segmentation and an automated quantification workflow. Existing public segmentation tools are not designed for comprehensive lower extremity CT analysis, particularly for clinically important inter/intramuscular adipose tissue, and most public methods only provide mask prediction rather than an end-to-end quantification system. To address this problem, we present LegSegNet, a deep learning system for lower extremity CT tissue segmentation and body composition quantification. Given an input CT scan, LegSegNet segments bone, skeletal muscle, subcutaneous adipose tissue, and inter/intramuscular adipose tissue. It then computes quantitative tissue measurements for downstream analysis. We developed the segmentation model using 1,302 manually annotated CT slices and evaluated it on 900 held-out test slices, with all annotations reviewed by radiologists. We benchmark LegSegNet against a broad set of 2D segmentation methods, including CNN-based models, transformer-based models, and finetuned foundation models, and further evaluate its generalization on an external public CT dataset. LegSegNet achieves the best overall segmentation performance, with an average Dice score of 89.31 on the held-out test set. To our knowledge, LegSegNet is the first publicly available end-to-end system for lower extremity CT tissue segmentation and quantification, providing a practical evaluation tool for future computer vision research in medical image analysis. The code and model weights are available at: https://github.com/mazurowski-lab/LegSegNet

Yuwen Chen, Yaqian Chen, Roy Colglazier +4

Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708 · Department of Radiology, Duke University, Durham, NC 27708 · Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27708 +2

Multi Organ Computed Tomography Segmentation Cone-Beam Computed Tomography Deep Learning Quantifying

May 28, 2026cs.CV

Towards the automated segmentation of epicardial and mediastinal fats: A multi-manufacturer approach using intersubject registration and random forest

The amount of fat on the surroundings of the heart is correlated to several health risk factors such as carotid stiffness, coronary artery calcification, atrial fibrillation, atherosclerosis, cancer incidence and others. Furthermore, the cardiac fat varies unrelated to the overall fat of the subject, and, therefore, it reinforces the quantitative analysis of these adipose tissues as being essential. Clinical decision support systems are computer programs capable of evaluating information and providing a corresponding diagnosis or data to complement the physicists' analyses. The aim of this work is to propose a method capable of fully automatically segmenting two types of cardiac adipose tissues that stand apart from each other by the pericardium on CT images obtained by the standard acquisition protocol used for coronary calcium scoring. Much effort was devoted to promote minimal user intervention and ease of reproducibility. The methodology proposed in this work consists of a registration, which will roughly adjust input images to a standard, an extraction of features related to pixels and their surrounding area and a segmentation step based on data mining classification algorithms that define if an incoming pixel is of a certain type. Experimentations showed that the achieved mean accuracy for the epicardial and mediastinal fats was 98.4% with a mean true positive rate of 96.2%. In average, the Dice similarity index was equal to 96.8%.

É. O. Rodrigues, A. Conci, F. F. C. Morais +1

Institute of Computing Universidade Federal Fluminense Niterói, Brazil · Institute of Medicine / Pró-Laudo Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil · Fac. de Ing. en Sist. Electr. e Ind. Universidad Técnica de Ambato Ambato, Ecuador

Echocardiography Multi Organ Computed Tomography Segmentation Cone-Beam Computed Tomography Random Forest Clinical Decision Support Controlled Comparison

May 20, 2026cs.CV

SpineContextResUNet: A Computationally Efficient Residual UNet for Spine CT Segmentation

Automated segmentation of the vertebral column in Computed Tomography (CT) scans is a prerequisite for pathological assessment and surgical planning. However, state-of-the-art methods, particularly those based on Transformers or large-scale ensembles, demand substantial GPU resources, creating a barrier for clinical adoption in resource-constrained environments or on edge devices. To address this, we introduce SpineContextResUNet, a computationally efficient 3D Residual U-Net designed for rapid spinal localization. Our architecture integrates a lightweight Context Block that employs parallel multi-dilated convolutions to capture long-range anatomical dependencies without the high latency of Recurrent Neural Networks (RNNs) or the memory overhead of Self-Attention mechanisms. Extensive validation on two public benchmarks, VerSe2020 and CTSpine1K, demonstrates that our model achieves a Dice score of 88.17% and 88.13% respectively. To evaluate performance under strict hardware constraints, we compared our model against a bottlenecked SwinUNETR scaled to match our ~1.7M hardware footprint. While the constrained Transformer suffers severe performance degradation due to a lack of spatial inductive biases in a limited-data regime, our CNN-based approach successfully maintains high accuracy. Crucially, heavy baselines like TotalSegmentator fail due to memory exhaustion on commodity hardware (Intel Core i5, 8GB RAM), our model performs robust inference, making it a viable solution for point-of-care diagnostics and deployment on edge platforms like the Nvidia Jetson Orin Nano.

K S Nithurshen, Saurabh J. Shigwan

Shiv Nadar University, Delhi NCR, India

Multi Organ Computed Tomography Segmentation U-Net Spatio-Temporal Transformers Long-Range Coherence

May 19, 2026eess.IV

Disentangling Sampling from Training Budget in Class-Imbalanced CT Body Composition Segmentation

Class imbalance is a fundamental challenge in medical image segmentation, where frequent classes typically dominate training at the expense of rare classes. Loss-based approaches mitigate imbalance by reweighting the per-pixel loss within the batch, while sampling strategies control which images enter the batch. Yet neither explicitly controls which classes appear within the batch, leaving rare-class exposure only partially rebalanced. In this work, we adopt episodic sampling from few-shot learning to promote class-balanced batch construction in a fully supervised setting. We decouple episodic sampling from its conventional metric-learning context and evaluate it in body composition segmentation in CT. We compare episodic sampling against random and weighted sampling on nine muscle and adipose tissues, derived from 210 scans of the public SAROS dataset. Training is performed under full- and low-data regimes, with additional comparisons under matched training iteration budgets. Under full-data training, all three strategies performed comparably (mean Dice 0.882 for episodic, 0.878 for random and weighted). Under low-data training, episodic sampling outperformed random and weighted (0.787 vs. 0.758 and 0.762), driven by a 12-fold difference in training iterations. Under matched training budgets, random and weighted overfit earlier, while episodic improved for approximately three times more iterations before plateauing. Our findings identify the training iteration budget as under-recognized confound in sampling strategies, motivating iteration-aware evaluation protocols for small datasets. Furthermore, the residual advantage of episodic sampling is consistent with an implicit regularization effect of class-balanced batches, offering a low-cost, model-agnostic strategy for class-imbalanced medical image segmentation. Code is available at https://github.com/iasonsky/episodic-sampling.

Iason Skylitsis, Dimitrios Karkalousos, Ivana Išgum

Department of Biomedical Engineering & Physics Amsterdam University Medical Center Amsterdam, The Netherlands · Informatics Institute, Faculty of Science University of Amsterdam Amsterdam, The Netherlands · Department of Radiology Mayo Clinic Rochester, United States

Multi Organ Computed Tomography Segmentation Rarity

May 19, 2026cs.CV

Cardiac fat segmentation using computed tomography and an image-to-image conditional generative adversarial neural network

In recent years, research has highlighted the association between increased adipose tissue surrounding the human heart and elevated susceptibility to cardiovascular diseases such as atrial fibrillation and coronary heart disease. However, the manual segmentation of these fat deposits has not been widely implemented in clinical practice due to the substantial workload it entails for medical professionals and the associated costs. Consequently, the demand for more precise and time-efficient quantitative analysis has driven the emergence of novel computational methods for fat segmentation. This study presents a novel deep learning-based methodology that offers autonomous segmentation and quantification of two distinct types of cardiac fat deposits. The proposed approach leverages the pix2pix network, a generative conditional adversarial network primarily designed for image-to-image translation tasks. By applying this network architecture, we aim to investigate its efficacy in tackling the specific challenge of cardiac fat segmentation, despite not being originally tailored for this purpose. The two types of fat deposits of interest in this study are referred to as epicardial and mediastinal fats, which are spatially separated by the pericardium. The experimental results demonstrated an average accuracy of 99.08% and f1-score 98.73 for the segmentation of the epicardial fat and 97.90% of accuracy and f1-score of 98.40 for the mediastinal fat. These findings represent the high precision and overlap agreement achieved by the proposed methodology. In comparison to existing studies, our approach exhibited superior performance in terms of f1-score and run time, enabling the images to be segmented in real time.

Guilherme Santos da Silva, Dalcimar Casanova, Jefferson Tales Oliva +1

Academic Department of Informatics, Universidade Tecnoldgica Federal do Parand (UTFPR), Pato Branco, 85503-390, Brasil · Graduate Program of Production and Systems Engineering, Universidade Tecnológica Federal do Parand (UTFPR), Pato Branco, 85503-390, Brazil

Echocardiography Multi Organ Computed Tomography Segmentation Generative Adversarial Network Long-Tailed Distribution

May 16, 2026cs.CV

Statistical Hand Shape Modeling from Clinical CT Scans Using Deep Learning and Implicit Skinning

Accurate segmentation and statistical shape modeling of hand anatomy have significant implications for medical diagnostics, ergonomics, and biomechanics. This study proposes an AI-assisted reconstruction pipeline for segmenting and analyzing hand anatomy from 1,271 elbow-to-hand (e2h-CT) computed tomography scans. A Pix2Pix-based conditional generative adversarial network is first employed to remove plaster cast and background artifacts from CT volumes. The cleaned scans are then processed in 3D Slicer to extract skin and bone masks, which are converted into closed-surface mesh models. Segmented bone meshes are used to construct skeletal representations, enabling implicit skinning to align all hand models into a standardized anatomical configuration. Subsequently, non-rigid registration is performed on the hand skin surfaces using the Geodesic Based Coherent Point Drift++ (GBCPD++) algorithm to establish point-wise correspondence across subjects. Principal Component Analysis (PCA) is then applied to the registered models to quantify anatomical shape variability. The Pix2Pix preprocessing stage achieved a Dice coefficient of 0.9856 and an IoU of 0.9720 on the held-out test set. Statistical modeling was performed on a subset of 90 scans in which the fingers were fully visible and anatomically separated. The resulting statistical shape distributions demonstrate strong agreement with the U.S. Army Anthropometric Survey (ANSUR II), supporting the anatomical validity of the reconstructed models. The proposed methodology demonstrates significant potential for advancing biomechanical modeling, ergonomic optimization, prosthetic design, and precision medical diagnostics.

Gokce Guven, Hasan Fehmi Ates, Deniz Karasahin +1

Dept. of Computer Science and Engineering Özyeğgin University İstanbul, Türkiye · Dept. of Artificial Intelligence and Data Engineering Özyeğgin University İstanbul, Türkiye · Osteoid Inc. İstanbul, Türkiye

3D Hand Multi Organ Computed Tomography Segmentation Statistical Shape Model Cone-Beam Computed Tomography Skeleton Biomechanics+2

May 15, 2026eess.IV

Evaluation of Anatomical Shape Priors in Deep Learning-Based Cardiac Multi-Compartment Segmentation

Whole-heart multi-compartment CT segmentation is clinically important, but standard CNNs do not explicitly enforce anatomical plausibility. Based on statistics derived from the training data, we evaluate whether lightweight explicit shape priors, implemented as shape-aware losses and spatial label distribution heatmap-guided U-Net variants, improve 3D cardiac segmentation on MM-WHS CT and WHS++. Across all experiments, a standard 3D U-Net surprisingly remained a very strong baseline, with handcrafted priors yielding at best marginal and inconsistent changes and often degrading performance. These results suggest that the baseline already captures substantial implicit anatomical regularities and that future gains will likely require more expressive learned priors rather than simple handcrafted anatomical shape constraints.

Michael Hudler, Franz Thaler, Martin Urschler

Institute for Medical Informatics, Statistics and Documentation Medical University of Graz

Echocardiography Anatomical Priors Multi Organ Computed Tomography Segmentation U-Net Anatomy 3D Priors

May 14, 2026cs.CV

Med-DisSeg: Dispersion-Driven Representation Learning for Fine-Grained Medical Image Segmentation

Accurate medical image segmentation is fundamental to precision medicine, yet robust delineation remains challenging under heterogeneous appearances, ambiguous boundaries, and large anatomical variability. Similar intensity and texture patterns between targets and surrounding tissues often lead to blurred activations and unreliable separation. We attribute these failures to representation collapse during encoding and insufficient fine grained multi scale decoding. To address these issues, we propose Med DisSeg, a dispersion driven medical image segmentation framework that jointly improves representation learning and anatomical delineation. Med DisSeg combines a lightweight Dispersive Loss with adaptive attention for fine grained structure segmentation. The Dispersive Loss enlarges inter sample margins by treating in batch hidden representations as negative pairs, producing well dispersed and boundary aware embeddings with negligible overhead. Based on these enhanced representations, the encoder strengthens structure sensitive responses, while the decoder performs adaptive multi scale calibration to preserve complementary local texture and global shape information. Extensive experiments on five datasets spanning three imaging modalities demonstrate consistent state of the art performance. Moreover, Med DisSeg achieves competitive results on multi organ CT segmentation, supporting its robustness and cross task applicability.

Zhiquan Chen, Haitao Wang, Guowei Zou +1

School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China · Guangdong Key Laboratory of Big Data Analysis and Processing, Guangzhou, China

Semi-Supervised Medical Image Segmentation Multi Organ Computed Tomography Segmentation Representation Learning Delineation Dispersion

May 9, 2026cs.CV

Reducing Annotation Burden for Femoral Cartilage Segmentation in Knee MRI via Cross-Sequence Transfer Learning

Purpose: To develop and evaluate cross-sequence transfer learning for automatic femoral cartilage segmentation, testing bidirectional transfer between dual-echo steady-state (DESS) and sagittal proton density-weighted 3D fast spin-echo (Cube) sequences. Materials and Methods: We optimized a modified 2D U-Net on 507 DESS images from the Osteoarthritis Initiative (OAI). We then established same-sequence baselines using subject-level cross-validation on a subset of 44 OAI DESS images and 44 Cube images acquired at the Istituto Ortopedico Rizzoli, Bologna, Italy. Each subset included 22 non-lesioned and 22 lesioned subjects. Finally, we performed transfer learning across sequences by fine-tuning the pretrained models on the target sequence with increasing training set sizes to study convergence, while keeping validation and test sets fixed. Segmentations were evaluated using Dice similarity coefficient (DSC) and average surface distance (ASD). Lesion effects were assessed with two-sided Mann-Whitney U tests with Bonferroni correction. Results: Same-sequence training yielded higher accuracy on DESS than Cube (DSC,

0.900

vs

0.830

;

P < .001

). Cube-to-DESS transfer matched DESS performance (DSC,

0.903 \pm 0.032

vs

0.900 \pm 0.027

), reaching a performance plateau at 9 training subjects. DESS-to-Cube yielded a lower combined DSC (

0.802 \pm 0.049

vs

0.830 \pm 0.042

), reaching a plateau at 24 training subjects. Lesions did not affect DESS (

P \ge .39

) but reduced Cube accuracy (DSC,

0.805

vs

0.856

;

P < .001

). Conclusion: Transfer learning across sequences can substantially reduce target-sequence annotation requirements for femoral cartilage segmentation, but performance is direction- and sequence-dependent, and the effects of lesions on segmentation may vary across MRI sequences.

Francesco Chiumento, Gianluigi Crimi, Elisa Moretta +7

School of Electronic Engineering, Dublin City University, Dublin, Ireland · Bioengineering and Computing Laboratory, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy · Dipartimento di Scienze Mediche e Chirurgiche (DIMEC), Alma Mater Studiorum – Università di Bologna, Bologna, Italy +4

Multi Organ Computed Tomography Segmentation Magnetic Resonance Imaging Transfer Learning

May 6, 2026q-bio.BM

Enhancing Cryo-EM Density Map Segmentation in Phenix for Improved Atomic Model Building

We introduce PhenixCraft, a fully automated pipeline for building atomic models from cryo-EM density maps. By integrating AlphaFold predictions, we enhance the map-segmentation step in Phenix during model building, addressing challenges posed by noise and artifacts that traditionally hinder this step. Our results demonstrate PhenixCraft's superior performance in TM-scores and sequence accuracy, significantly improving upon the limitations and inefficiencies of traditional model building using Phenix.

Chenwei Zhang

Department of Computer Science The University of British Columbia Vancouver, Canada

Cryo-Electron Microscopy Multi Organ Computed Tomography Segmentation Atoms Building Information Modeling Craft

May 4, 2026cs.CV

One Sequence to Segment Them All: Efficient Data Augmentation for CT and MRI Cross-Domain 3D Spine Segmentation

Deep learning-based medical image segmentation is increasingly used to support clinical diagnosis and develop new treatment strategies. However, model performance remains limited by the scarcity of high-quality annotated data and insufficient generalization across imaging protocols. This limitation is particularly evident in MRI and CT, where models are typically trained on a single acquisition sequence and exhibit reduced robustness when applied to unseen sequences or contrasts. Although data augmentation is widely used to improve general robustness on medical images, its impact on cross-modality generalization has not been quantitatively explored. In this work, we study a targeted set of data augmentation techniques designed to improve cross-modality transfer. We train three spine segmentation models, each on a single-modality/sequence dataset, and evaluate them across seven out-of-distribution datasets (spanning CT and MRI), reflecting a realistic single-sequence training and multi-sequence/contrast/modality deployment scenario. Our results demonstrate substantial performance gains on unseen domains (average Dice gain of 155 %) while preserving in-domain accuracy (average Dice decrease of 0.008 %), including effective transfer between CT and MRI. To mitigate the computational cost typically associated with strong data augmentation, we implement GPU-optimized augmentations that maintain, and even improve, training efficiency by approximately 10 %. We release our approach as an open-source toolbox, enabling seamless integration into commonly used frameworks such as nnUNet and MONAI. These augmentations significantly enhance robustness to heterogeneous clinical imaging scenarios without compromising training speed.

Nathan Molinier, Hendrik Möller, Thomas Dagonneau +6

NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal · Mila – Quebec AI Institute · Department for Interventional and Diagnostic Neuroradiology, TUM UniversityMay Hospital +3

Multi Organ Computed Tomography Segmentation Data Augmentation Magnetic Resonance Imaging Medical Imaging Cross-Modality

Apr 30, 2026cs.CV

MSR:Hybrid Field Modeling for CT-MRI Rigid-Deformable Registration of the Cervical Spine with an Annotated Dataset

Accurate CT-MRI registration of the cervical spine is essential for preoperative planning because this region is anatomically complex,highly variable,and vulnerable to injury of the vertebral arteries and spinal cord. However,cervical CT-MRI registration remains underexplored,particularly for rigid-deformable hybrid modeling,and the lack of high-quality annotated multimodal data further limits progress. To address these challenges, we construct and release a comprehensively annotated CT-MRI dataset, R-D-Reg, and propose MSR, a rigid-deformable hybrid registration framework for complex joint structures. Specifically, MSR includes a rigid registration module for independent local rigid alignment of individual vertebrae and a deformable registration module with an MSL block that combines Mamba-based global modeling and Swin Transformer-based local modeling through adaptive gating. The rigid and deformable deformation fields are then fused to generate a hybrid field that better preserves local anatomical consistency. The code and dataset are publicly available at https://github.com/ssc1230609-spec/MSR-registration.

Bohai Zhang, Wenjie Chen, Mu Li +8

School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, China. · Guangdong Provincial Key Laboratory of Medical Image Processing, Guangzhou, 510515, China. · Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology Guangzhou, 510515, China. +2

Magnetic Resonance Imaging Dataset Image Registration Multi Organ Computed Tomography Segmentation Deformation

Apr 29, 2026cs.CV

Virtual-reality based patient-specific simulation of spine surgical procedures: A fast, highly automated and high-fidelity system for surgical education and planning

Surgical training involves didactic teaching, mentor-led learning, surgical skills laboratories, and direct exposure to surgery; however, increasing clinical pressures have limited operating room (OR) exposure. This work leverages virtual reality (VR) to provide a safe and immersive training environment. Existing VR training is often based on standardized scenarios not tailored to individual clinical cases. This study addresses this limitation using artificial intelligence (AI) based computer vision methods to generate patient-specific simulations from computed tomography (CT) and magnetic resonance imaging (MRI). This study focuses on patient-specific spinal decompression simulation for spinal stenosis in a virtual operating room. The objectives were (1) automatic creation of 3D anatomical models and (2) VR simulation of spinal decompression procedures including laminectomy, disc resection, and foraminotomy. Model construction required multimodal fusion (registration) of CT and MRI and segmentation of relevant structures. Segmentation was evaluated using the Dice Similarity Coefficient (DSC), and registration accuracy using Target Registration Error (TRE). Qualitative feedback was obtained from surgeons and trainees. High-fidelity patient-specific 3D models were generated efficiently (approximately 2.5 minutes per case, N = 15). Segmentation accuracy was high, with a DSC of 0.95 (+/- 0.03) for vertebral bone and 0.895 (+/- 0.02) for soft tissue structures. Registration accuracy showed a mean TRE of 1.73 (+/- 0.42) mm. Semi-structured interviews indicated improved spatial understanding, increased procedural confidence, and strong perceived educational value. This platform significantly reduced the time and costs of patient-specific modelling, thereby facilitating pre-operative planning, post-procedural assessments, and comprehensive surgical simulation.

Raj Kumar Ranabhat, Tayler D Ross, Tony Jiao +3

Holland Bone and Joint Program, Sunnybrook Research Institute, Toronto, Canada. · Division of Orthopaedic Surgery, Department of Surgery, University of Toronto, Toronto, Canada. · Division of Spine Surgery, Sunnybrook Health Sciences Centre, Toronto, Canada.

Virtual Reality Simulated Patients Multi Organ Computed Tomography Segmentation Surgery High-Fidelity

Apr 20, 2026cs.CV

AI Approach for MRI-only Full-Spine Vertebral Segmentation and 3D Reconstruction in Paediatric Scoliosis

MRI is preferred over CT in paediatric imaging because it avoids ionising radiation, but its use in spine deformity assessment is largely limited by the lack of automated, high-resolution 3D bony reconstruction, which continues to rely on CT. MRI-based 3D reconstruction remains impractical due to manual workflows and the scarcity of labelled full-spine datasets. This study introduces an AI framework that enables fully automated thoracolumbar spine (T1-L5) segmentation and 3D reconstruction from MRI alone. Historical low-dose CT scans from adolescent idiopathic scoliosis (AIS) patients were converted into MRI-like images using a GAN and combined with existing labelled thoracic MRI data to train a U-Net-based model. The resulting algorithm accurately generated continuous thoracolumbar 3D reconstructions, improved segmentation accuracy (88% Dice score), and reduced processing time from approximately 1 hour to under one minute, while preserving AIS-specific deformity features. This approach enables radiation-free 3D deformity assessment from MRI, supporting clinical evaluation, surgical planning, and navigation in paediatric spine care.

Nathasha Naranpanawa, Maree T. Izatt, Robert D. Labrom +2

1Biomechanics and Spine Research Group, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane · Centre for Biomedical Technologies, School of Mechanical, Medical and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane · 3Orthopaedics Department, Queensland Children’s Hospital, Brisbane, Australia

Multi Organ Computed Tomography Segmentation 3D Reconstruction

Apr 16, 2026eess.IV

CTSCAN: Evaluation Leakage in Chest CT Segmentation and a Reproducible Patient-Disjoint Benchmark

Reported chest CT segmentation performance can be strongly inflated when train and test partitions mix slices from the same study. We present CTSCAN, a reproducible multi-source chest CT benchmark and research stack designed to measure what survives under patient-disjoint evaluation. The current four-class artifact aggregates 89 cases from PleThora, MedSeg SIRM, and LongCIU, and we show that the original slice-PNG workflow induces near-complete case reuse across train, validation, and test. Using the playground environment, we run a multi-seed protocol sweep with the same FPN plus EfficientNet-B0 control configuration under slice-mixed and case-disjoint evaluation. Across 3 seeds and 12 epochs per seed, the slice-mixed protocol reaches 0.6665 foreground Dice and 0.5031 foreground IoU, whereas the case-disjoint protocol reaches 0.2066 Dice and 0.1181 IoU. Removing patient reuse therefore reduces foreground Dice by 0.4599 absolute (69.00% relative) and foreground IoU by 0.3850 absolute (76.52% relative). CTSCAN packages the corrected benchmark with deterministic split manifests, explicit weak-supervision controls, a scripted multi-seed protocol sweep, and reproducible figure generation, providing a reusable basis for patient-disjoint chest CT evaluation.

Anton Ivchenko

Multi Organ Computed Tomography Segmentation Cone-Beam Computed Tomography Data Leakage

Feb 23, 2026cs.CV

Segmenting Low-Contrast XCTs of Concrete: An Unsupervised Approach

X-Ray Computed Tomography (XCT) is a compelling tool in experimental mechanics, capable of non-destructively extracting information pertaining to the internal morphology of materials. For materials with random heterogeneous morphology such as concrete, such information is of particular relevance since it allows for studies of morphology-related behaviour and for predictive modelling. Nevertheless, XCT images require semantic segmentation for practical usage. Here, concrete poses a unique challenge due to the similar X-ray attenuation coefficients of aggregates and mortar, which result in low contrast between the two phases in the ensuing XCT images. As such, purely intensity-dependent semantic segmentation tools remain unfeasible. While vision transformers (ViTs) and convolutional neural networks (CNNs) are proven techniques for semantic segmentation in such challenging cases, they typically require labelled training data, which is often unavailable for concrete or resource-intensive to obtain, thereby limiting their relevance. To address this challenge, a self-annotation technique is presented here that leverages superpixel algorithms to identify perceptually similar local regions in an image and relates them to the global context by utilizing the receptive field of a CNN-based model. This enables the model to learn a global-local relationship in the images and facilitates the identification of semantically similar structures. When evaluated against manually annotated ground truth on out-of-distribution data, the proposed methodology consistently outperformed direct greyscale thresholding across all pertinent metrics, demonstrating improved discernibility between aggregates and mortar, and providing the most favourable balance of sensitivity and precision for aggregate-phase identification.

Kaustav Das, Gaston Rauchs, Jan Sykora +1

Department of Mechanics, Faculty of Civil Engineering, Czech Technical University in Prague, Thákurova 7, 166 29 Prague 6, Czech Republic · Structural Composites Unit, Luxembourg Institute of Science and Technology (LIST), 5 avenue des Hauts-Fourneaux L-4362 Esch-sur-Alzette, Luxembourg

Multi Organ Computed Tomography Segmentation Semantic Segmentation Cone-Beam Computed Tomography High-Order Correlations

Jan 21, 2026cs.CV

Tracing 3D Anatomy in 2D Strokes: A Multi-Stage Projection Driven Approach to Cervical Spine Fracture Identification

Cervical spine fractures require rapid and accurate diagnosis, yet automatic CT interpretation remains challenging as subtle injuries must be assessed across large 3D volumes. We ask whether full 3D vertebra segmentation is necessary for automated fracture recognition, or whether vertebra masks approximated from 2D projections can preserve sufficient diagnostic context. We propose an end-to-end pipeline that localizes the cervical spine, estimates C1-C7 vertebra masks from optimized 2D projections, and uses the resulting vertebra-level volumes for downstream fracture classification. A YOLOv8 detector first localizes spine regions of interest from multi-view variance projections, achieving a 3D mean Intersection over Union of 94.45%. Multi-label vertebra segmentation is then performed with a DenseNet121-Unet on energy-based sagittal and coronal projections, attaining a mean Dice score of 87.86%. The predicted 2D masks are back-projected and fused into approximate 3D masks for each vertebra to extract volumes of interest from the original CT. These volumes are analyzed by an ensemble of 2.5D spatio-sequential CNN-Transformer models, yielding vertebra-level and patient-level F1 scores of 68.15 and 82.26, area under the receiver operating characteristic curve of 91.62 and 90.95, and area under the precision-recall curve of 75.60 and 92.00, respectively. The projection-derived volumes achieved fracture-recognition performance comparable to a full 3D-segmentation baseline, while shifting the vertebra segmentation stage into a lower-dimensional domain. Saliency-based explainability and interobserver variability analysis further examine interpretability and reliability. Overall, the results indicate that projection-based mask approximation is a viable proxy for full 3D vertebra segmentation in cervical fracture recognition.

Fabi Nahian Madhurja, Rusab Sarmun, Muhammad E. H. Chowdhury +3

Department of Computer Science and Engineering, BRAC University, Dhaka 1212, Bangladesh · Department of Electrical and Electronic Engineering, University of Dhaka, Dhaka 1000, Bangladesh · Department of Electrical Engineering, Qatar University, Doha 2713, Qatar +1

Multi Organ Computed Tomography Segmentation Cone-Beam Computed Tomography Anatomy Volume

Dec 29, 2023cs.CV

The TopCoW Challenge -- Topology-Aware Circle of Willis Segmentation for CT and MR Angiography

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to influence the risk, severity, and outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy remains a manual and time-consuming expert task. The CoW is commonly imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), yet few datasets with annotated CoW anatomy exist, and there have been no established benchmarks for comparing CoW segmentation algorithms. We organized the TopCoW benchmark challenge alongside the release of an annotated CoW dataset with 125 paired MRA and CTA scans from the same patients. Voxel-level annotations for 13 vessel components were created using virtual reality technology and verified by clinical experts. Participants submitted algorithms for CoW segmentation and variant classification, which we evaluated on internal and external test sets comprising 226 scans from over five centers. The benchmark includes voxel-level segmentation, CoW component detection, CoW variant classification, and two clinical application tasks. We received submissions from over 250 participants across six continents. Top-performing teams achieved over 90% Dice scores for CoW segmentation, over 80% F1 scores for detecting key vessel components, and over 70% balanced accuracy in CoW variant classification across nearly all test sets. The best algorithms also supported clinically relevant downstream tasks by accurately classifying fetal-type posterior cerebral arteries and localizing aneurysms in relation to CoW anatomy. This benchmark demonstrated the utility of CoW segmentation algorithms for some downstream clinical applications with explainability.

Kaiyuan Yang, Fabio Musio, Yihui Ma +112

Coronary Angiography Multi Organ Computed Tomography Segmentation Voxel

Date pendingeess.IV

Subcortical Masks Generation in CT Images via Ensemble-Based Cross-Domain Label Transfer

Subcortical segmentation in neuroimages plays an important role in understanding brain anatomy and facilitating computer-aided diagnosis of traumatic brain injuries and neurodegenerative disorders. However, training accurate automatic models requires large amounts of labelled data. Despite the availability of publicly available subcortical segmentation datasets for Magnetic Resonance Imaging (MRI), a significant gap exists for Computed Tomography (CT). This paper proposes an automatic ensemble framework to generate high-quality subcortical segmentation labels for CT scans by leveraging existing MRI-based models. We introduce a robust ensembling pipeline to integrate them and apply it to unannotated paired MRI-CT data, resulting in a comprehensive CT subcortical segmentation dataset. Extensive experiments on multiple public datasets demonstrate the superior performance of our proposed framework. Furthermore, using our generated CT dataset, we train segmentation models that achieve improved performance on related segmentation tasks. To facilitate future research, we make our source code, generated dataset, and trained models publicly available at https://github.com/alxw0671/CT_Subcortical_Segmentation, marking the first open-source release for CT subcortical segmentation to the best of our knowledge.

Augustine X. W. Lee, Pak-Hei Yeung, Jagath C. Rajapakse

College of Computing and Data Science, Nanyang Technological University, Singapore

Multi Organ Computed Tomography Segmentation Cone-Beam Computed Tomography