A 3D deep learning approach to epicardial fat segmentation in non-contrast and post-contrast cardiac CT images.
Ontology highlight
ABSTRACT:
SUBMITTER: Siriapisith T
PROVIDER: S-EPMC8670388 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundHigh quality 3D information of the microscopic plant tissue morphology-the spatial organization of cells and intercellular spaces in tissues-helps in understanding physiological processes in a wide variety of plants and tissues. X-ray micro-CT is a valuable tool that is becoming increasingly available in plant research to obtain 3D microstructural information of the intercellular pore space and individual pore sizes and shapes of tissues. However, individual cell morphology is difficult to retrieve from micro-CT as cells cannot be segmented properly due to negligible density differences at cell-to-cell interfaces. To address this, deep learning-based models were trained and tested to segment individual cells using X-ray micro-CT images of parenchyma tissue samples from apple and pear fruit with different cell and porosity characteristics.ResultsThe best segmentation model achieved an Aggregated Jaccard Index (AJI) of 0.86 and 0.73 for apple and pear tissue, respectively, which is an improvement over the current benchmark method that achieved AJIs of 0.73 and 0.67. Furthermore, the neural network was able to detect other plant tissue structures such as vascular bundles and stone cell clusters (brachysclereids), of which the latter were shown to strongly influence the spatial organization of pear cells. Based on the AJIs, apple tissue was found to be easier to segment, as the porosity and specific surface area of the pore space are higher and lower, respectively, compared to pear tissue. Moreover, samples with lower pore network connectivity, proved very difficult to segment.ConclusionsThe proposed method can be used to automatically quantify 3D cell morphology of plant tissue from micro-CT instead of opting for laborious manual annotations or less accurate segmentation approaches. In case fruit tissue porosity or pore network connectivity is too low or the specific surface area of the pore space too high, native X-ray micro-CT is unable to provide proper marker points of cell outlines, and one should rely on more elaborate contrast-enhancing scan protocols.
| S-EPMC10799452 | biostudies-literature
Project description:With the development of hybrid imaging scanners, micro-CT is widely used in locating abnormalities, studying drug metabolism, and providing structural priors to aid image reconstruction in functional imaging. Due to the low contrast of soft tissues, segmentation of soft tissue organs from mouse micro-CT images is a challenging problem. In this paper, we propose a mouse segmentation scheme based on dynamic contrast enhanced micro-CT images. With a homemade fast scanning micro-CT scanner, dynamic contrast enhanced images were acquired before and after injection of non-ionic iodinated contrast agents (iohexol). Then the feature vector of each voxel was extracted from the signal intensities at different time points. Based on these features, the heart, liver, spleen, lung, and kidney could be classified into different categories and extracted from separate categories by morphological processing. The bone structure was segmented using a thresholding method. Our method was validated on seven BALB/c mice using two different classifiers: a support vector machine classifier with a radial basis function kernel and a random forest classifier. The results were compared to manual segmentation, and the performance was assessed using the Dice similarity coefficient, false positive ratio, and false negative ratio. The results showed high accuracy with the Dice similarity coefficient ranging from 0.709 ± 0.078 for the spleen to 0.929 ± 0.006 for the kidney.
| S-EPMC5217965 | biostudies-literature
Project description:In this paper, we propose a framework for CT image segmentation of oil rock core. According to the characteristics of CT image of oil rock core, the existing level set segmentation algorithm is improved. Firstly, an algorithm of Chan-Vese (C-V) model is carried out to segment rock core from image background. Secondly the gray level of image background region is replaced by the average gray level of rock core, so that image background does not affect the binary segmentation. Next, median filtering processing is carried out. Finally, an algorithm of local binary fitting (LBF) model is executed to obtain the crack region. The proposed algorithm has been applied to oil rock core CT images with promising results.
| S-EPMC8516274 | biostudies-literature
Project description:The segmentation of organs at risk is a crucial and time-consuming step in radiotherapy planning. Good automatic methods can significantly reduce the time clinicians have to spend on this task. Due to its variability in shape and low contrast to surrounding structures, segmenting the parotid gland is challenging. Motivated by the recent success of deep learning, we study the use of two-dimensional (2-D), 2-D ensemble, and three-dimensional (3-D) U-Nets for segmentation. The mean Dice similarity to ground truth is ?0.83 for all three models. A patch-based approach for class balancing seems promising for false-positive reduction. The 2-D ensemble and 3-D U-Net are applied to the test data of the 2015 MICCAI challenge on head and neck autosegmentation. Both deep learning methods generalize well onto independent data (Dice 0.865 and 0.88) and are superior to a selection of model- and atlas-based methods with respect to the Dice coefficient. Since appropriate reference annotations are essential for training but often difficult and expensive to obtain, it is important to know how many samples are needed for training. We evaluate the performance after training with different-sized training sets and observe no significant increase in the Dice coefficient for more than 250 training cases.
| S-EPMC6165912 | biostudies-literature
Project description:Several studies have focused on the role of epicardial fat in the pathogenesis of cardiovascular disease (CVD). The main purpose of the study was to evaluate a computerized method for the quantitative analysis of epicardial fat volume (EFV) by non-contrast cardiac CT (NCT) for coronary calcium scan and coronary CT angiography (coronary CTA).Thirty patients (61±12.5 years, 73% male, body mass index (BMI) =25.9±6.3 kg/m2) referred to our Institution for suspected coronary artery disease (CAD) underwent NCT and coronary CTA. Epicardial boundaries were traced by 2 experienced operators (operator 1, operators 2) on 3 and 6 short-axis (SA) slices. EFV was computed with a semi-automatic method using an in-house developed software based on spherical harmonic representation of the epicardial surface. In order to analyze the inter-observer variability both the Coefficient of Repeatability (CR) and Intra Class Correlation (ICC) were computed.The total EFV was 103.62±50.97 and 94.96±67.91 cc in NCT and coronary CTA with non-significant difference (P=0.292). CR error was 10.22 cc for operator 1 and 11.31 cc for operator 2 in NCT and 7.99 cc for operator 1 and 7.75 cc for operator 2 in coronary CTA. To analyze the inter-observer variability CR and ICC were computed. CR was 8.17 and 8.39 cc with NCT and 7.07 and 7.21 cc with CTA for 6 and 3 SA slices respectively. ICC values >0.99 were obtained in all cases. The right ventricular EFV was 67.23±31.4 and 57.41±34.3 cc for NCT and coronary CTA respectively; the corresponding values for left ventricular EFV were 38.01±19.1 and 35.27±25.9 cc.Both NCT and coronary CTA can be used with low intra- and inter-observer variability for computer-assisted measurements of EFV. Cardiac CT may allow a fast and reliable computation of EFV in clinical setting.
| S-EPMC5537129 | biostudies-other
Project description:Segmentation of diseased liver remains a challenging task in clinical applications due to the high inter-patient variability in liver shapes, sizes and pathologies caused by cancers or other liver diseases. In this paper, we present a multi-resolution mesh segmentation algorithm for 3D segmentation of livers, called iterative mesh transformation that deforms the mesh of a region-of-interest (ROI) in a progressive manner by iterations between mesh transformation and contour optimization. Mesh transformation deforms the 3D mesh based on the deformation transfer model that searches the optimal mesh based on the affine transformation subjected to a set of constraints of targeting vertices. Besides, contour optimization searches the optimal transversal contours of the ROI by applying the dynamic-programming algorithm to the intersection polylines of the 3D mesh on 2D transversal image planes. The initial constraint set for mesh transformation can be defined by a very small number of targeting vertices, namely landmarks, and progressively updated by adding the targeting vertices selected from the optimal transversal contours calculated in contour optimization. This iterative 3D mesh transformation constrained by 2D optimal transversal contours provides an efficient solution to a progressive approximation of the mesh of the targeting ROI. Based on this iterative mesh transformation algorithm, we developed a semi-automated scheme for segmentation of diseased livers with cancers using as little as five user-identified landmarks. The evaluation study demonstrates that this semi-automated liver segmentation scheme can achieve accurate and reliable segmentation results with significant reduction of interaction time and efforts when dealing with diseased liver cases.
| S-EPMC4450142 | biostudies-literature
Project description:Purpose To compare epicardial fat in patients with arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) with that in healthy subjects. Materials and Methods In this retrospective study, cardiac CT scans in 44 patients with ARVD/C (mean age, 39 years ± 12; 23 men) were compared with those in 45 control group participants between January 2008 and July 2015. Volumes of intrathoracic adipose tissue, mediastinal adipose tissue (MAT), and total epicardial adipose tissue (EAT) were quantified. EAT was subdivided into three regions-right ventricular (RV) EAT, left ventricular (LV) EAT, and peri-atrial EAT (atrial EAT)-and normalized to MAT for all regions. Logistic regression and receiver operating characteristic analysis were performed to evaluate the association between epicardial fat with the diagnosis of ARVD/C. Results Total EAT volume was higher in patients with ARVD/C than in healthy control group participants (median, 98 mL vs 76 mL, respectively; P = .04). Regionally, LV and RV EAT volumes were higher in patients with ARVD/C than in control group participants, most notably when indexed to MAT (median LV EAT index: 0.49 vs 0.15, respectively; median RV EAT index: 0.91 vs 0.52; P ? .0005 for both). The optimal cutoff for diagnosis of ARVD/C was an LV EAT index of 0.24, with a sensitivity and specificity of 91% and 71%, respectively. Atrial EAT volume and total intrathoracic adipose tissue volume were not different between groups. RV diameter showed a positive correlation with total EAT index and LV EAT index (r = 0.21, P = .05 and r = 0.33, P = .002, respectively). Conclusion Higher amounts of right ventricular and left ventricular epicardial fat are found in hearts with arrhythmogenic right ventricular dysplasia/cardiomyopathy, particularly adjacent to the left ventricle, which correlates with disease severity and helps differentiate patients from healthy subjects. © RSNA, 2018 Online supplemental material is available for this article.
| S-EPMC6276062 | biostudies-literature
Project description:Early intervention in kidney cancer helps to improve survival rates. Abdominal computed tomography (CT) is often used to diagnose renal masses. In clinical practice, the manual segmentation and quantification of organs and tumors are expensive and time-consuming. Artificial intelligence (AI) has shown a significant advantage in assisting cancer diagnosis. To reduce the workload of manual segmentation and avoid unnecessary biopsies or surgeries, in this paper, we propose a novel end-to-end AI-driven automatic kidney and renal mass diagnosis framework to identify the abnormal areas of the kidney and diagnose the histological subtypes of renal cell carcinoma (RCC). The proposed framework first segments the kidney and renal mass regions by a 3D deep learning architecture (Res-UNet), followed by a dual-path classification network utilizing local and global features for the subtype prediction of the most common RCCs: clear cell, chromophobe, oncocytoma, papillary, and other RCC subtypes. To improve the robustness of the proposed framework on the dataset collected from various institutions, a weakly supervised learning schema is proposed to leverage the domain gap between various vendors via very few CT slice annotations. Our proposed diagnosis system can accurately segment the kidney and renal mass regions and predict tumor subtypes, outperforming existing methods on the KiTs19 dataset. Furthermore, cross-dataset validation results demonstrate the robustness of datasets collected from different institutions trained via the weakly supervised learning schema.
| S-EPMC9854669 | biostudies-literature
Project description:PURPOSE:We evaluated the feasibility of using an automatic segmentation tool to delineate cardiac substructures from noncontrast computed tomography (CT) images for cardiac dosimetry and toxicity analyses for patients with nonsmall cell lung cancer (NSCLC) after radiotherapy. MATERIAL AND METHODS:We used an in-house developed multi-atlas segmentation tool to delineate 11cardiac substructures, including the whole heart, four heart chambers, and six greater vessels, automatically from the averaged 4D-CT planning images of 49 patients with NSCLC. Two experienced radiation oncologists edited the auto-segmented contours. Times for automatic segmentation and modification were recorded. The modified contours were compared with the auto-segmented contours in terms of Dice similarity coefficient (DSC) and mean surface distance (MSD) to evaluate the extent of modification. Differences in dose-volume histogram (DVH) characteristics were also evaluated for the modified versus auto-segmented contours. RESULTS:The mean automatic segmentation time for all 11 structures was 7-9?min. For the 49 patients, the mean DSC values (±SD) ranged from .73?±?.08 to .95?±?.04, and the mean MSD values ranged from 1.3?±?.6?mm to 2.9?±?5.1?mm. Overall, the modifications were small; the largest modifications were in the pulmonary vein and the inferior vena cava. The heart V30 (volume receiving dose ?30?Gy) and the mean dose to the whole heart and the four heart chambers were not different for the modified versus the auto-segmented contours based on the statistically significant condition of p?<?.05. Also, the maximum dose to the great vessels was no different except for the pulmonary vein. CONCLUSIONS:Automatic segmentation of cardiac substructures did not require substantial modifications. Dosimetric evaluation showed no significant difference between the auto-segmented and modified contours for most structures, which suggests that the auto-segmented contours can be used to study cardiac dose-responses in clinical practice.
| S-EPMC6377299 | biostudies-literature
Project description:ObjectivesTo develop and evaluate a fully automatic method to measure diameters of the ascending and descending aorta on non-ECG-gated, non-contrast computed tomography (CT) scans.Material and methodsThe method combines multi-atlas registration to obtain seed points, aorta centerline extraction, and an optimal surface segmentation approach to extract the aorta surface around the centerline. From the extracted 3D aorta segmentation, the diameter of the ascending and descending aorta was calculated at cross-sectional slices perpendicular to the extracted centerline, at the level of the pulmonary artery bifurcation, and at 1-cm intervals up to 3 cm above and below this level. Agreement with manual annotations was evaluated by dice similarity coefficient (DSC) for segmentation overlap, mean surface distance (MSD), and intra-class correlation (ICC) of diameters on 100 CT scans from a lung cancer screening trial. Repeatability of the diameter measurements was evaluated on 617 baseline-one year follow-up CT scan pairs.ResultsThe agreement between manual and automatic segmentations was good with 0.95 ± 0.01 DSC and 0.56 ± 0.08 mm MSD. ICC between the diameters derived from manual and from automatic segmentations was 0.97, with the per-level ICC ranging from 0.87 to 0.94. An ICC of 0.98 for all measurements and per-level ICC ranging from 0.91 to 0.96 were obtained for repeatability.ConclusionThis fully automatic method can assess diameters in the thoracic aorta reliably even in non-ECG-gated, non-contrast CT scans. This could be a promising tool to assess aorta dilatation in screening and in clinical practice.Key points• Fully automatic method to assess thoracic aorta diameters. • High agreement between fully automatic method and manual segmentations. • Method is suitable for non-ECG-gated CT and can therefore be used in screening.
| S-EPMC6682850 | biostudies-literature