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Ultrasound imaging has shown promise in assessing synovium inflammation associated early stages of rheumatoid arthritis (RA). The precise identification of the synovium and the quantification of inflammation-specific imaging biomarkers is a crucial aspect of accurately quantifying and grading RA. In this study, a deep learning-based approach is presented that automates the segmentation of the synovium in ultrasound images of finger joints affected by RA. Two convolutional neural network architectures for image segmentation were trained and validated in a limited number of 2-D images, extracted from N = 18 3-D ultrasound volumes acquired from N = 9 RA patients, with sparse ground truth annotations of the synovium. Various augmentation strategies were employed to enhance the diversity and size of the training dataset. The utilization of geometric and noise augmentation transforms resulted in the highest dice score (0.768 ±0.031,N=6),andintersectionoverunion(0.624±0.040, N = 6), as determined via six-fold cross-validation. In addition, the segmentation model is used to generate dense 3-D segmentation maps in the ultrasound volumes, based on the available sparse annotations. The developed technique shows promise in facilitating more efficient and standardized workflow for RA screening using ultrasound imaging.

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Liver segmentation technologies play vital roles in clinical diagnosis, disease monitoring, and surgical planning due to the complex anatomical structure and physiological functions of the liver. This paper provides a comprehensive review of the developments, challenges, and future directions in liver segmentation technology. We systematically analyzed high-quality research published between 2014 and 2024, focusing on liver segmentation methods, public datasets, and evaluation metrics. This review highlights the transition from manual to semi-automatic and fully automatic segmentation methods, describes the capabilities and limitations of available technologies, and provides future outlooks.

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Diffusion tensor imaging (DTI) can provide unique contrast and insight into microstructural changes with age or disease of the hippocampus, although it is difficult to measure the hippocampus because of its comparatively small size, location, and shape. This has been markedly improved by the advent of a clinically feasible 1-mm isotropic resolution 6-min DTI protocol at 3 T of the hippocampus with limited brain coverage of 20 axial-oblique slices aligned along its long axis. However, manual segmentation is too laborious for large population studies, and it cannot be automatically segmented directly on the diffusion images using traditional T1 or T2 image-based methods because of the limited brain coverage and different contrast. An automatic method is proposed here that segments the hippocampus directly on high-resolution diffusion images based on an extension of well-known deep learning architectures like UNet and UNet++ by including additional dense residual connections. The method was trained on 100 healthy participants with previously performed manual segmentation on the 1-mm DTI, then evaluated on typical healthy participants (n = 53), yielding an excellent voxel overlap with a Dice score of ~ 0.90 with manual segmentation; notably, this was comparable with the inter-rater reliability of manually delineating the hippocampus on diffusion magnetic resonance imaging (MRI) (Dice score of 0.86). This method also generalized to a different DTI protocol with 36% fewer acquisitions. It was further validated by showing similar age trajectories of volumes, fractional anisotropy, and mean diffusivity from manual segmentations in one cohort (n = 153, age 5-74 years) with automatic segmentations from a second cohort without manual segmentations (n = 354, age 5-90 years). Automated high-resolution diffusion MRI segmentation of the hippocampus will facilitate large cohort analyses and, in future research, needs to be evaluated on patient groups.

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This work presents the application of an Encoder-Decoder convolutional neural network (ED-CNN) model to automatically segment COVID-19 computerised tomography (CT) data. By doing so we are producing an alternative model to current literature, which is easy to follow and reproduce, making it more accessible for real-world applications as little training would be required to use this. Our simple approach achieves results comparable to those of previously published studies, which use more complex deep-learning networks. We demonstrate a high-quality automated segmentation prediction of thoracic CT scans that correctly delineates the infected regions of the lungs. This segmentation automation can be used as a tool to speed up the contouring process, either to check manual contouring in place of a peer checking, when not possible or to give a rapid indication of infection to be referred for further treatment, thus saving time and resources. In contrast, manual contouring is a time-consuming process in which a professional would contour each patient one by one to be later checked by another professional. The proposed model uses approximately 49 k parameters while others average over 1,000 times more parameters. As our approach relies on a very compact model, shorter training times are observed, which make it possible to easily retrain the model using other data and potentially afford "personalised medicine" workflows. The model achieves similarity scores of Specificity (Sp) = 0.996 ± 0.001, Accuracy (Acc) = 0.994 ± 0.002 and Mean absolute error (MAE) = 0.0075 ± 0.0005.

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We aim to develop a deep learning-based algorithm for automated segmentation of thigh muscles and subcutaneous adipose tissue (SAT) from T1-weighted muscle MRIs from patients affected by muscular dystrophies (MDs). From March 2019 to February 2022, adult and pediatric patients affected by MDs were enrolled from Azienda Ospedaliera Universitaria Pisana, Pisa, Italy (Institution 1) and the IRCCS Stella Maris Foundation, Calambrone-Pisa, Italy (Institution 2), respectively. All patients underwent a bilateral thighs MRI including an axial T1 weighted in- and out-of-phase (dual-echo). Both muscles and SAT were manually and separately segmented on out-of-phase image sets by a radiologist with 6 years of experience in musculoskeletal imaging. A U-Net1 and U-Net3 were built to automatically segment the SAT, all the thigh muscles together and the three muscular compartments separately. The dataset was randomly split into the on train, validation, and test set. The segmentation performance was assessed through the Dice similarity coefficient (DSC). The final cohort included 23 patients. The estimated DSC for U-Net1 was 96.8%, 95.3%, and 95.6% on train, validation, and test set, respectively, while the estimated accuracy for U-Net3 was 94.1%, 92.9%, and 93.9%. Both of the U-Nets achieved a median DSC of 0.95 for SAT segmentation. The U-Net1 and the U-Net3 achieved an optimal agreement with manual segmentation for the automatic segmentation. The so-developed neural networks have the potential to automatically segment thigh muscles and SAT in patients affected by MDs.

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Background: Magnetic resonance imaging (MRI) cartilage transverse relaxation time (T2) reflects cartilage composition, mechanical properties, and early osteoarthritis (OA). T2 analysis requires cartilage segmentation. In this study, we clinically validate fully automated T2 analysis at 1.5 Tesla (T) in anterior cruciate ligament (ACL)-injured and healthy knees. Methods: We studied 71 participants: 20 ACL-injured patients with, and 22 without dynamic knee instability, 13 with surgical reconstruction, and 16 healthy controls. Sagittal multi-echo-spin-echo (MESE) MRIs were acquired at baseline and 1-year follow-up. Femorotibial cartilage was segmented manually; a convolutional neural network (CNN) algorithm was trained on MRI data from the same scanner. Results: Dice similarity coefficients (DSCs) of automated versus manual segmentation in the 71 participants were 0.83 (femora) and 0.89 (tibiae). Deep femorotibial T2 was similar between automated (45.7±2.6 ms) and manual (45.7±2.7 ms) segmentation (P=0.828), whereas superficial layer T2 was slightly overestimated by automated analysis (53.2±2.2 vs. 52.1±2.1 ms for manual; P<0.001). T2 correlations were r=0.91-0.99 for deep and r=0.86-0.97 for superficial layers across regions. The only statistically significant T2 increase over 1 year was observed in the deep layer of the lateral femur [standardized response mean (SRM) =0.58 for automated vs. 0.52 for manual analysis; P<0.001]. There was no relevant difference in baseline/longitudinal T2 values/changes between the ACL-injured groups and healthy participants, with either segmentation method. Conclusions: This clinical validation study suggests that automated cartilage T2 analysis from MESE at 1.5T is technically feasible and accurate. More efficient 3D sequences and longer observation intervals may be required to detect the impact of ACL injury induced joint instability on cartilage composition (T2).

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OBJECTIVE: Segmentation, the partitioning of patient imaging into multiple, labeled segments, has several potential clinical benefits but when performed manually is tedious and resource intensive. Automated deep learning (DL)-based segmentation methods can streamline the process. The objective of this study was to evaluate a label-efficient DL pipeline that requires only a small number of annotated scans for semantic segmentation of sinonasal structures in CT scans. STUDY DESIGN: Retrospective cohort study. SETTING: Academic institution. METHODS: Forty CT scans were used in this study including 16 scans in which the nasal septum (NS), inferior turbinate (IT), maxillary sinus (MS), and optic nerve (ON) were manually annotated using an open-source software. A label-efficient DL framework was used to train jointly on a few manually labeled scans and the remaining unlabeled scans. Quantitative analysis was then performed to obtain the number of annotated scans needed to achieve submillimeter average surface distances (ASDs). RESULTS: Our findings reveal that merely four labeled scans are necessary to achieve median submillimeter ASDs for large sinonasal structures-NS (0.96 mm), IT (0.74 mm), and MS (0.43 mm), whereas eight scans are required for smaller structures-ON (0.80 mm). CONCLUSION: We have evaluated a label-efficient pipeline for segmentation of sinonasal structures. Empirical results demonstrate that automated DL methods can achieve submillimeter accuracy using a small number of labeled CT scans. Our pipeline has the potential to improve pre-operative planning workflows, robotic- and image-guidance navigation systems, computer-assisted diagnosis, and the construction of statistical shape models to quantify population variations. LEVEL OF EVIDENCE: N/A.

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BACKGROUND AND PURPOSE: Conclusions from prior literature regarding the impact of sex, age, and height on spinal cord (SC) MRI morphometrics are conflicting, while the effect of body weight on SC morphometrics has been found to be nonsignificant. The purpose of this case-control study is to assess the associations between cervical SC MRI morphometric parameters and age, sex, height, and weight to establish their potential role as confounding variables in a clinical study of people with multiple sclerosis (MS) compared to a cohort of healthy volunteers. METHODS: Sixty-nine healthy volunteers and 31 people with MS underwent cervical SC MRI at 3 Tesla field strength. Images were centered at the C3/C4 intervertebral disc and processed using Spinal Cord Toolbox v.4.0.2. Mixed-effects linear regression models were used to evaluate the effects of biological variables and disease status on morphometric parameters. RESULTS: Sex, age, and height had significant effects on cord and gray matter (GM) cross-sectional area (CSA) as well as the GM:cord CSA ratio. There were no significant effects of body weight on morphometric parameters. The effect of MS disease duration on cord CSA in the C4 level was significant when controlling for all other variables. CONCLUSIONS: Studies of disease-related changes in SC morphometry should control for sex, age, and height to account for physiological variation.

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Blowout fractures are common midfacial fractures in which one or several of the bones of orbital vault break. This is usually caused by a direct trauma to the eye with a blunt object such as a fist. Fracturing of the fragile orbital bones can lead to changes in the orbital volume, which may cause enophthalmos, diplopia, and impaired facial aesthetics. Objectives: The aim of this study is to investigate whether there is an association between volume change of the bony orbit and age, gender, or trauma mechanism. Methods: A retrospective study of patients with unilateral blowout or blow-in fractures treated and examined in Päijät-Häme Central Hospital, Lahti, Finland was conducted. Altogether, 127 patients met the inclusion criteria. Their computed tomographs (CT) were measured with an orbit-specific automated segmentation-based volume measurement tool, and the relative orbital volume change between fractured and intact orbital vault was calculated. Thereafter, a statistical analysis was performed. A p-value less than 0.05 was considered significant. Results: We found that relative increase in orbital volume and age have a statistically significant association (p = 0.022). Trauma mechanism and gender showed no significant role. Conclusions: Patient's age is associated with increased volume change in fractures of the bony orbit.

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INTRODUCTION: Traumatic bone marrow lesions (BML) are frequently identified on knee MRI scans in patients following an acute full-thickness, complete ACL tear. BMLs coincide with regions of elevated localized bone loss, and studies suggest these may act as a precursor to the development of post-traumatic osteoarthritis. This study addresses the labour-intensive manual assessment of BMLs by using a 3D U-Net for automated identification and segmentation from MRI scans. METHODS: A multi-task learning approach was used to segment both bone and BML from T2 fat-suppressed (FS) fast spin echo (FSE) MRI sequences for BML assessment. Training and testing utilized datasets from individuals with complete ACL tears, employing a five-fold cross-validation approach and pre-processing involved image intensity normalization and data augmentation. A post-processing algorithm was developed to improve segmentation and remove outliers. Training and testing datasets were acquired from different studies with similar imaging protocol to assess the model's performance robustness across different populations and acquisition conditions. RESULTS: The 3D U-Net model exhibited effectiveness in semantic segmentation, while post-processing enhanced segmentation accuracy and precision through morphological operations. The trained model with post-processing achieved a Dice similarity coefficient (DSC) of 0.75 ± 0.08 (mean ± std) and a precision of 0.87 ± 0.07 for BML segmentation on testing data. Additionally, the trained model with post-processing achieved a DSC of 0.93 ± 0.02 and a precision of 0.92 ± 0.02 for bone segmentation on testing data. This demonstrates the approach's high accuracy for capturing true positives and effectively minimizing false positives in the identification and segmentation of bone structures. CONCLUSION: Automated segmentation methods are a valuable tool for clinicians and researchers, streamlining the assessment of BMLs and allowing for longitudinal assessments. This study presents a model with promising clinical efficacy and provides a quantitative approach for bone-related pathology research and diagnostics.

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Accurate resection cavity segmentation on MRI is important for neuroimaging research involving epilepsy surgical outcomes. Manual segmentation, the gold standard, is highly labour intensive. Automated pipelines are an efficient potential solution; however, most have been developed for use following temporal epilepsy surgery. Our aim was to compare the accuracy of four automated segmentation pipelines following surgical resection in a mixed cohort of subjects following temporal or extra temporal epilepsy surgery. We identified 4 open-source automated segmentation pipelines. Epic-CHOP and ResectVol utilise SPM-12 within MATLAB, while Resseg and Deep Resection utilise 3D U-net convolutional neural networks. We manually segmented the resection cavity of 50 consecutive subjects who underwent epilepsy surgery (30 temporal, 20 extratemporal). We calculated Dice similarity coefficient (DSC) for each algorithm compared to the manual segmentation. No algorithm identified all resection cavities. ResectVol (n = 44, 88 %) and Epic-CHOP (n = 42, 84 %) were able to detect more resection cavities than Resseg (n = 22, 44 %, P < 0.001) and Deep Resection (n = 23, 46 %, P < 0.001). The SPM-based pipelines (Epic-CHOP and ResectVol) performed better than the deep learning-based pipelines in the overall and extratemporal surgery cohorts. In the temporal cohort, the SPM-based pipelines had higher detection rates, however there was no difference in the accuracy between methods. These pipelines could be applied to machine learning studies of outcome prediction to improve efficiency in pre-processing data, however human quality control is still required.

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BACKGROUND: Myopia affects 1.4 billion individuals worldwide. Notably, there is increasing evidence that choroidal thickness plays an important role in myopia and risk of developing myopia-related conditions. With the advancements in artificial intelligence (AI), choroidal thickness segmentation can now be automated, offering inherent advantages such as better repeatability, reduced grader variability, and less reliance for manpower. Hence, we aimed to evaluate the agreement between AI-automated and manual segmented measurements of subfoveal choroidal thickness (SFCT) using two swept-source optical coherence tomography (OCT) systems. METHODS: Subjects aged ≥ 16 years, with myopia of ≥ 0.50 diopters in both eyes, were recruited from the Prospective Myopia Cohort Study in Singapore (PROMYSE). OCT scans were acquired using Triton DRI-OCT and PLEX Elite 9000. OCT images were segmented both automatically with an established SA-Net architecture and manually using a standard technique with adjudication by two independent graders. SFCT was subsequently determined based on the segmentation. The Bland-Altman plot and intraclass correlation coefficient (ICC) were used to evaluate the agreement. RESULTS: A total of 229 subjects (456 eyes) with mean [± standard deviation (SD)] age of 34.1 (10.4) years were included. The overall SFCT (mean ± SD) based on manual segmentation was 216.9 ± 82.7 µm with Triton DRI-OCT and 239.3 ± 84.3 µm with PLEX Elite 9000. ICC values demonstrated excellent agreement between AI-automated and manual segmented SFCT measurements (PLEX Elite 9000: ICC = 0.937, 95% CI: 0.922 to 0.949, P < 0.001; Triton DRI-OCT: ICC = 0.887, 95% CI: 0.608 to 0.950, P < 0.001). For PLEX Elite 9000, manual segmented measurements were generally thicker when compared to AI-automated segmented measurements, with a fixed bias of 6.3 µm (95% CI: 3.8 to 8.9, P < 0.001) and proportional bias of 0.120 (P < 0.001). On the other hand, manual segmented measurements were comparatively thinner than AI-automated segmented measurements for Triton DRI-OCT, with a fixed bias of - 26.7 µm (95% CI: - 29.7 to - 23.7, P < 0.001) and proportional bias of - 0.090 (P < 0.001). CONCLUSION: We observed an excellent agreement in choroidal segmentation measurements when comparing manual with AI-automated techniques, using images from two SS-OCT systems. Given its edge over manual segmentation, automated segmentation may potentially emerge as the primary method of choroidal thickness measurement in the future.

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PURPOSE: To propose a method for calculating hematoma volume based on automatic segmentation of chronic subdural hematoma (CSDH) using 3D U­net and investigate whether it can be used clinically to predict recurrence. METHODS: Hematoma volumes manually measured from pre- and postoperative computed tomography (CT) images were used as ground truth data to train 3D U­net in 200 patients (400 CT scans). A total of 215 patients (430 CT scans) were used as test data to output segmentation results from the trained 3D U­net model. The similarity with the ground truth data was evaluated using Dice scores for pre and postoperative separately. The recurrence prediction accuracy was evaluated by obtaining receiver operating characteristic (ROC) curves for the segmentation results. Using a typical mobile PC, the computation time per case was measured and the average time was calculated. RESULTS: The median Dice score of the test data were preoperative hematoma volume (Pre-HV): 0.764 and postoperative subdural cavity volume (Post-SCV): 0.741. In ROC analyses assessing recurrence prediction, the area under the curve (AUC) of the manual was 0.755 in Pre-HV, whereas the 3D U­net was 0.735. In Post-SCV, the manual AUC was 0.779; the 3D U­net was 0.736. No significant differences were found between manual and 3D U­net for all results. Using a mobile PC, the average time taken to output the test data results was 30 s per case. CONCLUSION: The proposed method is a simple, accurate, and clinically applicable; it can contribute to the widespread use of recurrence prediction scoring systems for CSDH.

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INTRODUCTION: This study aimed to evaluate the accuracy of our own artificial intelligence (AI)-generated model to assess automated segmentation and quantification of body composition-derived computed tomography (CT) slices from the lumber (L3) region in colorectal cancer (CRC) patients. METHODS: A total of 541 axial CT slices at the L3 vertebra were retrospectively collected from 319 patients with CRC diagnosed during 2012-2019 at a single Australian tertiary institution, Western Health in Melbourne. A two-dimensional U-Net convolutional network was trained on 338 slices to segment muscle, visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT). Manual reading of these same slices of muscle, VAT and SAT was created to serve as ground truth data. The Dice similarity coefficient was used to assess the U-Net-based segmentation performance on both a validation dataset (68 slices) and a test dataset (203 slices). The measurement of cross-sectional area and Hounsfield unit (HU) density of muscle, VAT and SAT were compared between two methods. RESULTS: The segmentation for muscle, VAT and SAT demonstrated excellent performance for both the validation (Dice similarity coefficients >0.98, respectively) and test (Dice similarity coefficients >0.97, respectively) datasets. There was a strong positive correlation between manual and AI segmentation measurements of body composition for both datasets (Spearman's correlation coefficients: 0.944-0.999, P < 0.001). CONCLUSIONS: Compared to the gold standard, this fully automated segmentation system exhibited a high accuracy for assessing segmentation and quantification of abdominal muscle and adipose tissues of CT slices at the L3 in CRC patients.

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Purpose: Aortic dissection carries a mortality as high as 50%, but surgical palliation is also fraught with morbidity risks of stroke or paralysis. As such, a significant focus of medical decision making is on longitudinal aortic diameters. We hypothesize that three-dimensional (3D) modeling affords a more efficient methodology toward automated longitudinal aortic measurement. The first step is to automate the measurement of manually segmented 3D models of the aorta. We developed and validated an algorithm to analyze a 3D segmented aorta and output the maximum dimension of minimum cross-sectional areas in a stepwise progression from the diaphragm to the aortic root. Accordingly, the goal is to assess the diagnostic validity of the 3D modeling measurement as a substitute for existing 2D measurements. Approach: From January 2021 to June 2022, 66 3D non-contrast steady-state free precession magnetic resonance images of aortic pathology with clinical aortic measurements were identified; 3D aorta models were manually segmented. A novel mathematical algorithm was applied to each model to generate maximal aortic diameters from the diaphragm to the root, which were then correlated to clinical measurements. Results: With a 76% success rate, we analyzed the resulting 50 3D aortic models utilizing the automated measurement tool. There was an excellent correlation between the automated measurement and the clinical measurement. The intra-class correlation coefficient and p-value for each of the nine measured locations of the aorta were as follows: sinus of valsalva, 0.99, <0.001; sino-tubular junction, 0.89, <0.001; ascending aorta, 0.97, <0.001; brachiocephalic artery, 0.96, <0.001; transverse segment 1, 0.89, <0.001; transverse segment 2, 0.93, <0.001; isthmus region, 0.92, <0.001; descending aorta, 0.96, <0.001; and aorta at diaphragm, 0.3, <0.001. Conclusions: Automating diagnostic measurements that appease clinical confidence is a critical first step in a fully automated process. This tool demonstrates excellent correlation between measurements derived from manually segmented 3D models and the clinical measurements, laying the foundation for transitioning analytic methodologies from 2D to 3D.

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Researchers who study the human hippocampus are naturally interested in how its subfields function. However, many researchers are precluded from examining subfields because their manual delineation from magnetic resonance imaging (MRI) scans (still the gold standard approach) is time consuming and requires significant expertise. To help ameliorate this issue, we present here two protocols, one for 3T MRI and the other for 7T MRI, that permit automated hippocampus segmentation into six subregions, namely dentate gyrus/cornu ammonis (CA)4, CA2/3, CA1, subiculum, pre/parasubiculum, and uncus along the entire length of the hippocampus. These protocols are particularly notable relative to existing resources in that they were trained and tested using large numbers of healthy young adults (n = 140 at 3T, n = 40 at 7T) whose hippocampi were manually segmented by experts from MRI scans. Using inter-rater reliability analyses, we showed that the quality of automated segmentations produced by these protocols was high and comparable to expert manual segmenters. We provide full open access to the automated protocols, and anticipate they will save hippocampus researchers a significant amount of time. They could also help to catalyze subfield research, which is essential for gaining a full understanding of how the hippocampus functions.

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Background: Intracranial space is divided into three compartments by the falx cerebri and tentorium cerebelli. We assessed whether cerebrospinal fluid (CSF) distribution evaluated by a specifically developed deep-learning neural network (DLNN) could assist in quantifying mass effect. Methods: Head trauma CT scans from a high-volume emergency department between 2018 and 2020 were retrospectively analyzed. Manual segmentations of intracranial compartments and CSF served as the ground truth to develop a DLNN model to automate the segmentation process. Dice Similarity Coefficient (DSC) was used to evaluate the segmentation performance. Supratentorial CSF Ratio was calculated by dividing the volume of CSF on the side with reduced CSF reserve by the volume of CSF on the opposite side. Results: Two hundred and seventy-four patients (mean age, 61 years ± 18.6) after traumatic brain injury (TBI) who had an emergency head CT scan were included. The average DSC for training and validation datasets were respectively: 0.782 and 0.765. Lower DSC were observed in the segmentation of CSF, respectively 0.589, 0.615, and 0.572 for the right supratentorial, left supratentorial, and infratentorial CSF regions in the training dataset, and slightly lower values in the validation dataset, respectively 0.567, 0.574, and 0.556. Twenty-two patients (8%) had midline shift exceeding 5 mm, and 24 (8.8%) presented with high/mixed density lesion exceeding >25 ml. Fifty-five patients (20.1%) exhibited mass effect requiring neurosurgical treatment. They had lower supratentorial CSF volume and lower Supratentorial CSF Ratio (both p < 0.001). A Supratentorial CSF Ratio below 60% had a sensitivity of 74.5% and specificity of 87.7% (AUC 0.88, 95%CI 0.82-0.94) in identifying patients that require neurosurgical treatment for mass effect. On the other hand, patients with CSF constituting 10-20% of the intracranial space, with 80-90% of CSF specifically in the supratentorial compartment, and whose Supratentorial CSF Ratio exceeded 80% had minimal risk. Conclusion: CSF distribution may be presented as quantifiable ratios that help to predict surgery in patients after TBI. Automated segmentation of intracranial compartments using the DLNN model demonstrates a potential of artificial intelligence in quantifying mass effect. Further validation of the described method is necessary to confirm its efficacy in triaging patients and identifying those who require neurosurgical treatment.

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Quantitative computed tomography (QCT)-based in silico models have demonstrated improved accuracy in predicting hip fractures with respect to the current gold standard, the areal bone mineral density. These models require that the femur bone is segmented as a first step. This task can be challenging, and in fact, it is often almost fully manual, which is time-consuming, operator-dependent, and hard to reproduce. This work proposes a semi-automated procedure for femur bone segmentation from CT images. The proposed procedure is based on the bone and joint enhancement filter and graph-cut algorithms. The semi-automated procedure performances were assessed on 10 subjects through comparison with the standard manual segmentation. Metrics based on the femur geometries and the risk of fracture assessed in silico resulting from the two segmentation procedures were considered. The average Hausdorff distance (0.03 ± 0.01 mm) and the difference union ratio (0.06 ± 0.02) metrics computed between the manual and semi-automated segmentations were significantly higher than those computed within the manual segmentations (0.01 ± 0.01 mm and 0.03 ± 0.02). Besides, a blind qualitative evaluation revealed that the semi-automated procedure was significantly superior (p < 0.001) to the manual one in terms of fidelity to the CT. As for the hip fracture risk assessed in silico starting from both segmentations, no significant difference emerged between the two (R2 = 0.99). The proposed semi-automated segmentation procedure overcomes the manual one, shortening the segmentation time and providing a better segmentation. The method could be employed within CT-based in silico methodologies and to segment large volumes of images to train and test fully automated and supervised segmentation methods.

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Purpose: The objective of this study was to develop a fully automatic mass segmentation method called AMS-U-Net for digital breast tomosynthesis (DBT), a popular breast cancer screening imaging modality. The aim was to address the challenges posed by the increasing number of slices in DBT, which leads to higher mass contouring workload and decreased treatment efficiency. Approach: The study used 50 slices from different DBT volumes for evaluation. The AMS-U-Net approach consisted of four stages: image pre-processing, AMS-U-Net training, image segmentation, and post-processing. The model performance was evaluated by calculating the true positive ratio (TPR), false positive ratio (FPR), F-score, intersection over union (IoU), and 95% Hausdorff distance (pixels) as they are appropriate for datasets with class imbalance. Results: The model achieved 0.911, 0.003, 0.911, 0.900, 5.82 for TPR, FPR, F-score, IoU, and 95% Hausdorff distance, respectively. Conclusions: The AMS-U-Net model demonstrated impressive visual and quantitative results, achieving high accuracy in mass segmentation without the need for human interaction. This capability has the potential to significantly increase clinical efficiency and workflow in DBT for breast cancer screening.

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Recent advances in computing power triggered the use of artificial intelligence in image analysis in life sciences. To train these algorithms, a large enough set of certified labeled data is required. The trained neural network is then capable of producing accurate instance segmentation results that will then need to be re-assembled into the original dataset: the entire process requires substantial expertise and time to achieve quantifiable results. To speed-up the process, from cell organelle detection to quantification across electron microscopy modalities, we propose a deep-learning based approach for fast automatic outline segmentation (FAMOUS), that involves organelle detection combined with image morphology, and 3D meshing to automatically segment, visualize and quantify cell organelles within volume electron microscopy datasets. From start to finish, FAMOUS provides full segmentation results within a week on previously unseen datasets. FAMOUS was showcased on a HeLa cell dataset acquired using a focused ion beam scanning electron microscope, and on yeast cells acquired by transmission electron tomography. RESEARCH HIGHLIGHTS: Introducing a rapid, multimodal machine-learning workflow for the automatic segmentation of 3D cell organelles. Successfully applied to a variety of volume electron microscopy datasets and cell lines. Outperforming manual segmentation methods in time and accuracy. Enabling high-throughput quantitative cell biology.

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