The purpose of this study is to assess segmentation reproducibility of artificial intelligence-based algorithm, TotalSegmentator, across 34 anatomical structures using multiphasic abdominal CT scans comparing unenhanced, arterial, and portal venous phases in the same patients. A total of 1252 multiphasic abdominal CT scans acquired at our institution between January 1, 2012, and December 31, 2022, were retrospectively included. TotalSegmentator was used to derive volumetric measurements of 34 abdominal organs and structures from the total of 3756 CT series. Reproducibility was evaluated across three contrast phases per CT and compared to two human readers and an independent nnU-Net trained on the BTCV dataset. Relative deviation in segmented volumes and absolute volume deviations (AVD) were reported. Volume deviation within 5% was considered reproducible. Thus, non-inferiority testing was conducted using a 5% margin. Twenty-nine out of 34 structures had volume deviations within 5% and were considered reproducible. Volume deviations for the adrenal glands, gallbladder, spleen, and duodenum were above 5%. Highest reproducibility was observed for bones (- 0.58% [95% CI: - 0.58, - 0.57]) and muscles (- 0.33% [- 0.35, - 0.32]). Among abdominal organs, volume deviation was 1.67% (1.60, 1.74). TotalSegmentator outperformed the reproducibility of the nnU-Net trained on the BTCV dataset with an AVD of 6.50% (6.41, 6.59) vs. 10.03% (9.86, 10.20; p < 0.0001), most notably in cases with pathologic findings. Similarly, TotalSegmentator's AVD between different contrast phases was superior compared to the interreader AVD for the same contrast phase (p = 0.036). TotalSegmentator demonstrated high intra-individual reproducibility for most abdominal structures in multiphasic abdominal CT scans. Although reproducibility was lower in pathologic cases, it outperforms both human readers and a nnU-Net trained on the BTCV dataset.

Coronary artery disease (CAD) is a major worldwide health concern, contributing significantly to the global burden of cardiovascular diseases (CVDs). According to the 2023 World Health Organization (WHO) report, CVDs account for approximately 17.9 million deaths annually. This emphasizies the need for advanced diagnostic tools such as coronary computed tomography angiography (CCTA). The incorporation of deep learning (DL) technologies could significantly improve CCTA analysis by automating the quantification of plaque and stenosis, thus enhancing the precision of cardiac risk assessments. A recent meta-analysis highlights the evolving role of CCTA in patient management, showing that CCTA-guided diagnosis and management reduced adverse cardiac events and improved event-free survival in patients with stable and acute coronary syndromes. An extensive literature search was carried out across various electronic databases, such as MEDLINE, Embase, and the Cochrane Library. This search utilized a specific strategy that included both Medical Subject Headings (MeSH) terms and pertinent keywords. The review adhered to PRISMA guidelines and focused on studies published between 2019 and 2024 that employed deep learning (DL) for coronary computed tomography angiography (CCTA) in patients aged 18 years or older. After implementing specific inclusion and exclusion criteria, a total of 10 articles were selected for systematic evaluation regarding quality and bias. This systematic review included a total of 10 studies, demonstrating the high diagnostic performance and predictive capabilities of various deep learning models compared to different imaging modalities. This analysis highlights the effectiveness of these models in enhancing diagnostic accuracy in imaging techniques. Notably, strong correlations were observed between DL-derived measurements and intravascular ultrasound findings, enhancing clinical decision-making and risk stratification for CAD. Deep learning-enabled CCTA represents a promising advancement in the quantification of coronary plaques and stenosis, facilitating improved cardiac risk prediction and enhancing clinical workflow efficiency. Despite variability in study designs and potential biases, the findings support the integration of DL technologies into routine clinical practice for better patient outcomes in CAD management.

The prevalence of coronary artery disease (CAD) has become the major cause of death across the world in recent years. The accurate segmentation of coronary artery is important in clinical diagnosis and treatment of coronary artery disease (CAD) such as stenosis detection and plaque analysis. Deep learning techniques have been shown to assist medical experts in diagnosing diseases using biomedical imaging. There are many methods which employ 2D DL models for medical image segmentation. The 2D Pyramid Scene Parsing Neural Network (PSPNet) has potential in this domain but not explored for the segmentation of coronary arteries from 3D Coronary Computed Tomography Angiography (CCTA) images. The contribution of present research work is to propose the modification of 2D PSPNet into 3D PSPNet for segmenting the coronary arteries from 3D CCTA images. The innovative factor is to evaluate the network performance by employing Global processing and Patch based processing methods. The experimental results achieved a Dice Similarity Coefficient (DSC) of 0.76 for Global process method and 0.73 for Patch based method using a subset of 200 images from the ImageCAS dataset.

Vision Transformer shows great superiority in medical image segmentation due to the ability to learn long-range dependency. For medical image segmentation from 3-D data, such as computed tomography (CT), existing methods can be broadly classified into 2-D-based and 3-D-based methods. One key limitation in 2-D-based methods is that the intraslice information is ignored, while the limitation in 3-D-based methods is the high computation cost and memory consumption, resulting in a limited feature representation for inner slice information. During the clinical examination, radiologists primarily use the axial plane and then routinely review both axial and coronal planes to form a 3-D understanding of anatomy. Motivated by this fact, our key insight is to design a hybrid model that can first learn fine-grained inner slice information and then generate a 3-D understanding of anatomy by incorporating 3-D information. We present a novel Hybrid Residual TransFormer (HResFormer) for 3-D medical image segmentation. Building upon standard 2-D and 3-D Transformer backbones, HResFormer involves two novel key designs: 1) a Hybrid Local-Global fusion Module (HLGM) to effectively and adaptively fuse inner slice information from 2-D Transformers and intraslice information from 3-D volumes for 3-D Transformers with local fine-grained and global long-range representation and 2) residual learning of the hybrid model, which can effectively leverage the inner slice and intraslice information for better 3-D understanding of anatomy. Experiments show that our HResFormer outperforms prior art on widely used medical image segmentation benchmarks. This article sheds light on an important but neglected way to design Transformers for 3-D medical image segmentation.

Purpose: Accurate segmentation of clinical target volumes (CTV) and organs-at-risk is crucial for optimizing gynecologic brachytherapy (GYN-BT) treatment planning. However, anatomical variability, low soft-tissue contrast in CT imaging, and limited annotated datasets pose significant challenges. This study presents GynBTNet, a novel multi-stage learning framework designed to enhance segmentation performance through self-supervised pretraining and hierarchical fine-tuning strategies. Methods: GynBTNet employs a three-stage training strategy: (1) self-supervised pretraining on large-scale CT datasets using sparse submanifold convolution to capture robust anatomical representations, (2) supervised fine-tuning on a comprehensive multi-organ segmentation dataset to refine feature extraction, and (3) task-specific fine-tuning on a dedicated GYN-BT dataset to optimize segmentation performance for clinical applications. The model was evaluated against state-of-the-art methods using the Dice Similarity Coefficient (DSC), 95th percentile Hausdorff Distance (HD95), and Average Surface Distance (ASD). Results: Our GynBTNet achieved superior segmentation performance, significantly outperforming nnU-Net and Swin-UNETR. Notably, it yielded a DSC of 0.837 +/- 0.068 for CTV, 0.940 +/- 0.052 for the bladder, 0.842 +/- 0.070 for the rectum, and 0.871 +/- 0.047 for the uterus, with reduced HD95 and ASD compared to baseline models. Self-supervised pretraining led to consistent performance improvements, particularly for structures with complex boundaries. However, segmentation of the sigmoid colon remained challenging, likely due to anatomical ambiguities and inter-patient variability. Statistical significance analysis confirmed that GynBTNet's improvements were significant compared to baseline models.

Sarcopenia, or the loss of muscle quality and quantity, has been associated with poor clinical outcomes in liver transplantation such as infection, increased length of stay, and increased patient mortality. Abdominal computed tomography (CT) scans are utilized to measure patient core musculature as a measurement of sarcopenia. Methods to extract information on core body musculature can be through either freehand region-of-interest (ROI) or machine learning algorithms to quantitate total body muscle within a given area. This study directly compares these two collection methods leveraging length of stay (LOS) outcomes previously found to be associated with freehand ROI measurements. A total of 50 individuals were included who underwent liver transplantation from our single center between January 1, 2016, and May 30, 2021, and had a non-contrast abdominal CT scan within 6-months of surgery. CT-derived skeletal muscle measures at the third lumbar vertebrae were obtained using freehand ROI and an automated deep learning system. Correlation analysis of freehand psoas muscle measures, psoas area index (PAI) and mean Hounsfield units (mHU), were significantly correlated to the automated deep learning system's total skeletal muscle measures at the level of the L3, skeletal muscle index (SMI) and skeletal muscle density (SMD), respectively (R² = 0.4221; p value < 0.0001; R² = 0.6297; p value < 0.0001). The automated deep learning model's SMI predicted ∼20% of the variability (R² = 0.2013; hospital length of stay) while the PAI variable only predicted about 10% of the variability (R² = 0.0919; total healthcare length of stay) of the length of stay variables. In contrast, both the freehand ROI mHU and the automated deep learning model's muscle density variables were associated with ∼20% of the variability in the inpatient length of stay (R² = 0.2383 and 0.1810, respectively) and total healthcare length of stay variables (R² = 0.2190 and 0.1947, respectively). Sarcopenia measurements represent an important risk stratification tool for liver transplantation outcomes. For muscle sarcopenia assessment association with LOS, freehand measures of sarcopenia perform similarly to automated deep learning system measurements.

The clinical utility of body composition in predicting the severity of acute pancreatitis (AP) remains unclear. We aimed to measure body composition using artificial intelligence (AI) to predict severe AP in hospitalized patients. We performed a retrospective study of patients hospitalized with AP at three tertiary care centers in 2018. Patients with computer tomography (CT) imaging of the abdomen at admission were included. A fully automated and validated abdominal segmentation algorithm was used for body composition analysis. The primary outcome was severe AP, defined as having persistent single- or multi-organ failure as per the revised Atlanta classification. 352 patients were included. Severe AP occurred in 35 patients (9.9%). In multivariable analysis, adjusting for male sex and first episode of AP, intermuscular adipose tissue (IMAT) was associated with severe AP, OR = 1.06 per 5 cm², p = 0.0207. Subcutaneous adipose tissue (SAT) area approached significance, OR = 1.05, p = 0.17. Neither visceral adipose tissue (VAT) nor skeletal muscle (SM) was associated with severe AP. In obese patients, a higher SM was associated with severe AP in unadjusted analysis (86.7 vs 75.1 and 70.3 cm² in moderate and mild, respectively p = 0.009). In this multi-site retrospective study using AI to measure body composition, we found elevated IMAT to be associated with severe AP. Although SAT was non-significant for severe AP, it approached statistical significance. Neither VAT nor SM were significant. Further research in larger prospective studies may be beneficial.

Brain lesion segmentation is crucial for neurological disease research and diagnosis. As different types of lesions exhibit distinct characteristics on different imaging modalities, segmentation methods are typically developed in a task-specific manner, where each segmentation model is tailored to a specific lesion type and modality. However, the use of task-specific models requires predetermination of the lesion type and imaging modality, which complicates their deployment in real-world scenarios. In this work, we propose a universal foundation model for brain lesion segmentation on magnetic resonance imaging (MRI), which can automatically segment different types of brain lesions given input of various MRI modalities. We develop a novel Mixture of Modality Experts (MoME) framework with multiple expert networks attending to different imaging modalities. A hierarchical gating network is proposed to combine the expert predictions and foster expertise collaboration. Moreover, to avoid the degeneration of each expert network, we introduce a curriculum learning strategy during training to preserve the specialisation of each expert. In addition to MoME, to handle the combination of multiple input modalities, we propose MoME+, which uses a soft dispatch network for input modality routing. We evaluated the proposed method on nine brain lesion datasets, encompassing five imaging modalities and eight lesion types. The results show that our model outperforms state-of-the-art universal models for brain lesion segmentation and achieves promising generalisation performance onto unseen datasets.

In the field of gland segmentation in histopathology, deep-learning methods have made significant progress. However, most existing methods not only require a large amount of high-quality annotated data but also tend to confuse the internal of the gland with the background. To address this challenge, we propose a new semi-supervised method named DCCL-Seg for gland segmentation, which follows the teacher-student framework. Our approach can be divided into follows steps. First, we design a contrastive learning module to improve the ability of the student model's feature extractor to distinguish between gland and background features. Then, we introduce a Signed Distance Field (SDF) prediction task and employ dual-consistency strategy (across tasks and models) to better reinforce the learning of gland internal. Next, we proposed a pseudo label filtering and reweighting mechanism, which filters and reweights the pseudo labels generated by the teacher model based on confidence. However, even after reweighting, the pseudo labels may still be influenced by unreliable pixels. Finally, we further designed an assistant predictor to learn the reweighted pseudo labels, which do not interfere with the student model's predictor and ensure the reliability of the student model's predictions. Experimental results on the publicly available GlaS and CRAG datasets demonstrate that our method outperforms other semi-supervised medical image segmentation methods.

Fully-supervised deep neural networks have achieved remarkable progress in medical image segmentation, yet they heavily rely on extensive manually labeled data and exhibit inflexibility for unseen tasks. Few-shot segmentation (FSS) addresses these issues by predicting unseen classes from a few labeled support examples. However, most existing FSS models struggle to generalize to diverse target tasks distinct from training domains. Furthermore, designing promising network architectures for such tasks is expertise-intensive and laborious. In this paper, we introduce MOE-FewSeg, a novel automatic design method for FSS architectures. Specifically, we construct a U-shaped encoder-decoder search space that incorporates capabilities for information interaction and feature selection, thereby enabling architectures to leverage prior knowledge from publicly available datasets across diverse domains for improved prediction of various target tasks. Given the potential conflicts among disparate target tasks, we formulate the multi-task problem as a multi-objective optimization problem. We employ a multi-objective genetic algorithm to identify the Pareto-optimal architectures for these target tasks within this search space. Furthermore, to mitigate the impact of noisy labels due to dataset quality variations, we propose a noise-robust loss function named NRL, which encourages the model to de-emphasize larger loss values. Empirical results demonstrate that MOE-FewSeg outperforms manually designed architectures and other related approaches.