Deep Learning-Based Detection of Malformed Optic Chiasms From MRI Images
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ABSTRACT:
SUBMITTER: Puzniak R
PROVIDER: S-EPMC8573410 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:ObjectiveTo establish and evaluate the 3D U-Net model for automated segmentation and detection of pelvic bone metastases in patients with prostate cancer (PCa) using diffusion-weighted imaging (DWI) and T1 weighted imaging (T1WI) images.MethodsThe model consisted of two 3D U-Net algorithms. A total of 859 patients with clinically suspected or confirmed PCa between January 2017 and December 2020 were enrolled for the first 3D U-Net development of pelvic bony structure segmentation. Then, 334 PCa patients were selected for the model development of bone metastases segmentation. Additionally, 63 patients from January to May 2021 were recruited for the external evaluation of the network. The network was developed using DWI and T1WI images as input. Dice similarity coefficient (DSC), volumetric similarity (VS), and Hausdorff distance (HD) were used to evaluate the segmentation performance. Sensitivity, specificity, and area under the curve (AUC) were used to evaluate the detection performance at the patient level; recall, precision, and F1-score were assessed at the lesion level.ResultsThe pelvic bony structures segmentation on DWI and T1WI images had mean DSC and VS values above 0.85, and the HD values were <15 mm. In the testing set, the AUC of the metastases detection at the patient level were 0.85 and 0.80 on DWI and T1WI images. At the lesion level, the F1-score achieved 87.6% and 87.8% concerning metastases detection on DWI and T1WI images, respectively. In the external dataset, the AUC of the model for M-staging was 0.94 and 0.89 on DWI and T1WI images.ConclusionThe deep learning-based 3D U-Net network yields accurate detection and segmentation of pelvic bone metastases for PCa patients on DWI and T1WI images, which lays a foundation for the whole-body skeletal metastases assessment.
| S-EPMC8666439 | biostudies-literature
Project description:BackgroundDevelopment and validation of a deep learning method to automatically segment the peri-ampullary (PA) region in magnetic resonance imaging (MRI) images.MethodsA group of patients with or without periampullary carcinoma (PAC) was included. The PA regions were manually annotated in MRI images by experts. Patients were randomly divided into one training set, one validation set, and one test set. Deep learning methods were developed to automatically segment the PA region in MRI images. The segmentation performance of the methods was compared in the validation set. The model with the highest intersection over union (IoU) was evaluated in the test set.ResultsThe deep learning algorithm achieved optimal accuracies in the segmentation of the PA regions in both T1 and T2 MRI images. The value of the IoU was 0.68, 0.68, and 0.64 for T1, T2, and combination of T1 and T2 images, respectively.ConclusionsDeep learning algorithm is promising with accuracies of concordance with manual human assessment in segmentation of the PA region in MRI images. This automated non-invasive method helps clinicians to identify and locate the PA region using preoperative MRI scanning.
| S-EPMC8193851 | biostudies-literature
Project description:An increasing number of genetic and metabolic anomalies have been determined to lead to cancer, generally fatal. Cancerous cells may spread to any body part, where they can be life-threatening. Skin cancer is one of the most common types of cancer, and its frequency is increasing worldwide. The main subtypes of skin cancer are squamous and basal cell carcinomas, and melanoma, which is clinically aggressive and responsible for most deaths. Therefore, skin cancer screening is necessary. One of the best methods to accurately and swiftly identify skin cancer is using deep learning (DL). In this research, the deep learning method convolution neural network (CNN) was used to detect the two primary types of tumors, malignant and benign, using the ISIC2018 dataset. This dataset comprises 3533 skin lesions, including benign, malignant, nonmelanocytic, and melanocytic tumors. Using ESRGAN, the photos were first retouched and improved. The photos were augmented, normalized, and resized during the preprocessing step. Skin lesion photos could be classified using a CNN method based on an aggregate of results obtained after many repetitions. Then, multiple transfer learning models, such as Resnet50, InceptionV3, and Inception Resnet, were used for fine-tuning. In addition to experimenting with several models (the designed CNN, Resnet50, InceptionV3, and Inception Resnet), this study's innovation and contribution are the use of ESRGAN as a preprocessing step. Our designed model showed results comparable to the pretrained model. Simulations using the ISIC 2018 skin lesion dataset showed that the suggested strategy was successful. An 83.2% accuracy rate was achieved by the CNN, in comparison to the Resnet50 (83.7%), InceptionV3 (85.8%), and Inception Resnet (84%) models.
| S-EPMC9324455 | biostudies-literature
Project description:Deep learning has been demonstrated effective in many neuroimaging applications. However, in many scenarios, the number of imaging sequences capturing information related to small vessel disease lesions is insufficient to support data-driven techniques. Additionally, cohort-based studies may not always have the optimal or essential imaging sequences for accurate lesion detection. Therefore, it is necessary to determine which imaging sequences are crucial for precise detection. This study introduces a deep learning framework to detect enlarged perivascular spaces (ePVS) and aims to find the optimal combination of MRI sequences for deep learning-based quantification. We implemented an effective lightweight U-Net adapted for ePVS detection and comprehensively investigated different combinations of information from SWI, FLAIR, T1-weighted (T1w), and T2-weighted (T2w) MRI sequences. The experimental results showed that T2w MRI is the most important for accurate ePVS detection, and the incorporation of SWI, FLAIR and T1w MRI in the deep neural network had minor improvements in accuracy and resulted in the highest sensitivity and precision (sensitivity =0.82, precision =0.83). The proposed method achieved comparable accuracy at a minimal time cost compared to manual reading. The proposed automated pipeline enables robust and time-efficient readings of ePVS from MR scans and demonstrates the importance of T2w MRI for ePVS detection and the potential benefits of using multimodal images. Furthermore, the model provides whole-brain maps of ePVS, enabling a better understanding of their clinical correlates compared to the clinical rating methods within only a couple of brain regions.
| S-EPMC10078801 | biostudies-literature
Project description:Optic-disc photography (ODP) has proven to be very useful for optic nerve evaluation in glaucoma. In real clinical practice, however, limited patient cooperation, small pupils, or media opacities can limit the performance of ODP. The purpose of this study was to propose a deep-learning approach for increased resolution and improved legibility of ODP by contrast, color, and brightness compensation. Each high-resolution original ODP was transformed into two counterparts: (1) down-scaled 'low-resolution ODPs', and (2) 'compensated high-resolution ODPs' produced via enhancement of the visibility of the optic disc margin and surrounding retinal vessels using a customized image post-processing algorithm. Then, the differences between these two counterparts were directly learned through a super-resolution generative adversarial network (SR-GAN). Finally, by inputting the high-resolution ODPs into SR-GAN, 4-times-up-scaled and overall-color-and-brightness-transformed 'enhanced ODPs' could be obtained. General ophthalmologists were instructed (1) to assess each ODP's image quality, and (2) to note any abnormal findings, at 1-month intervals. The image quality score for the enhanced ODPs was significantly higher than that for the original ODP, and the overall optic disc hemorrhage (DH)-detection accuracy was significantly higher with the enhanced ODPs. We expect that this novel deep-learning approach will be applied to various types of ophthalmic images.
| S-EPMC7529226 | biostudies-literature
Project description:PurposeTo present fully automated DL-based prostate cancer detection system for prostate MRI.MethodsMRI scans from two institutions, were used for algorithm training, validation, testing. MRI-visible lesions were contoured by an experienced radiologist. All lesions were biopsied using MRI-TRUS-guidance. Lesions masks, histopathological results were used as ground truth labels to train UNet, AH-Net architectures for prostate cancer lesion detection, segmentation. Algorithm was trained to detect any prostate cancer ≥ ISUP1. Detection sensitivity, positive predictive values, mean number of false positive lesions per patient were used as performance metrics.Results525 patients were included for training, validation, testing of the algorithm. Dataset was split into training (n = 368, 70%), validation (n = 79, 15%), test (n = 78, 15%) cohorts. Dice coefficients in training, validation sets were 0.403, 0.307, respectively, for AHNet model compared to 0.372, 0.287, respectively, for UNet model. In validation set, detection sensitivity was 70.9%, PPV was 35.5%, mean number of false positive lesions/patient was 1.41 (range 0-6) for UNet model compared to 74.4% detection sensitivity, 47.8% PPV, mean number of false positive lesions/patient was 0.87 (range 0-5) for AHNet model. In test set, detection sensitivity for UNet was 72.8% compared to 63.0% for AHNet, mean number of false positive lesions/patient was 1.90 (range 0-7), 1.40 (range 0-6) in UNet, AHNet models, respectively.ConclusionWe developed a DL-based AI approach which predicts prostate cancer lesions at biparametric MRI with reasonable performance metrics. While false positive lesion calls remain as a challenge of AI-assisted detection algorithms, this system can be utilized as an adjunct tool by radiologists.
| S-EPMC10506420 | biostudies-literature
Project description:Crops require appropriate planting techniques at different growth stages. Judgments on crop maturity affect the yield of crops. The planting and management of crops rely heavily on experienced farmers, which can reduce planting costs and increase yields. With the advancement of smart agriculture [1], images of crops can be used to accurately determine the growth stage of crops and estimate crop yields [2]. This can be combined with drones or smartphones to predict the growth stage and yield of Fortunella margarita for farmers in the future. This article presents an F. margarita image dataset. We classified F. margarita into three growth stages: mature, immature, and growing. In this dataset, an image may contain plants in several growth stages. The images were divided into seven categories according to growth stage. The dataset contains a total of 1031 original images. The total number of images was increased to 6611 through data augmentation. In addition, the dataset includes 6611 annotations with 7 categories of manually marked positions of F. margarita. Field images were captured in Jiaoxi, Yilan County, Taiwan, using smartphones. The dataset can serve as a resource for researchers who use different algorithms of machine learning or deep learning for object detection, image segmentation, and multiclass classification.
| S-EPMC8385152 | biostudies-literature
Project description:Coronary artery disease (CAD) is one of the major causes of fatalities across the globe. The recent developments in convolutional neural networks (CNN) allow researchers to detect CAD from computed tomography (CT) images. The CAD detection model assists physicians in identifying cardiac disease at earlier stages. The recent CAD detection models demand a high computational cost and a more significant number of images. Therefore, this study intends to develop a CNN-based CAD detection model. The researchers apply an image enhancement technique to improve the CT image quality. The authors employed You look only once (YOLO) V7 for extracting the features. Aquila optimization is used for optimizing the hyperparameters of the UNet++ model to predict CAD. The proposed feature extraction technique and hyperparameter tuning approach reduces the computational costs and improves the performance of the UNet++ model. Two datasets are utilized for evaluating the performance of the proposed CAD detection model. The experimental outcomes suggest that the proposed method achieves an accuracy, recall, precision, F1-score, Matthews correlation coefficient, and Kappa of 99.4, 98.5, 98.65, 98.6, 95.35, and 95 and 99.5, 98.95, 98.95, 98.95, 96.35, and 96.25 for datasets 1 and 2, respectively. In addition, the proposed model outperforms the recent techniques by obtaining the area under the receiver operating characteristic and precision-recall curve of 0.97 and 0.95, and 0.96 and 0.94 for datasets 1 and 2, respectively. Moreover, the proposed model obtained a better confidence interval and standard deviation of [98.64-98.72] and 0.0014, and [97.41-97.49] and 0.0019 for datasets 1 and 2, respectively. The study's findings suggest that the proposed model can support physicians in identifying CAD with limited resources.
| S-EPMC10093692 | biostudies-literature
Project description:Brain tumor localization and segmentation from magnetic resonance imaging (MRI) are hard and important tasks for several applications in the field of medical analysis. As each brain imaging modality gives unique and key details related to each part of the tumor, many recent approaches used four modalities T1, T1c, T2, and FLAIR. Although many of them obtained a promising segmentation result on the BRATS 2018 dataset, they suffer from a complex structure that needs more time to train and test. So, in this paper, to obtain a flexible and effective brain tumor segmentation system, first, we propose a preprocessing approach to work only on a small part of the image rather than the whole part of the image. This method leads to a decrease in computing time and overcomes the overfitting problems in a Cascade Deep Learning model. In the second step, as we are dealing with a smaller part of brain images in each slice, a simple and efficient Cascade Convolutional Neural Network (C-ConvNet/C-CNN) is proposed. This C-CNN model mines both local and global features in two different routes. Also, to improve the brain tumor segmentation accuracy compared with the state-of-the-art models, a novel Distance-Wise Attention (DWA) mechanism is introduced. The DWA mechanism considers the effect of the center location of the tumor and the brain inside the model. Comprehensive experiments are conducted on the BRATS 2018 dataset and show that the proposed model obtains competitive results: the proposed method achieves a mean whole tumor, enhancing tumor, and tumor core dice scores of 0.9203, 0.9113 and 0.8726 respectively. Other quantitative and qualitative assessments are presented and discussed.
| S-EPMC8149837 | biostudies-literature
Project description:ObjectivesThis study aimed to investigate the accuracy of deep learning algorithms to diagnose tooth caries and classify the extension and location of dental caries in cone beam computed tomography (CBCT) images. To the best of our knowledge, this is the first study to evaluate the application of deep learning for dental caries in CBCT images.MethodsThe CBCT image dataset comprised 382 molar teeth with caries and 403 noncarious molar cases. The dataset was divided into a development set for training and validation and test set. Three images were obtained for each case, including axial, sagittal, and coronal. The test dataset was provided to a multiple-input convolutional neural network (CNN). The network made predictions regarding the presence or absence of dental decay and classified the lesions according to their depths and types for the provided samples. Accuracy, sensitivity, specificity, and F1 score values were measured for dental caries detection and classification.ResultsThe diagnostic accuracy, sensitivity, specificity, and F1 score for caries detection in carious molar teeth were 95.3%, 92.1%, 96.3%, and 93.2%, respectively, and for noncarious molar teeth were 94.8%, 94.3%, 95.8%, and 94.6%. The CNN network showed high sensitivity, specificity, and accuracy in classifying caries extensions and locations.ConclusionsThis research demonstrates that deep learning models can accurately identify dental caries and classify their depths and types with high accuracy, sensitivity, and specificity. The successful application of deep learning in this field will undoubtedly assist dental practitioners and patients in improving diagnostic and treatment planning in dentistry.Clinical significanceThis study showed that deep learning can accurately detect and classify dental caries. Deep learning can provide dental caries detection accurately. Considering the shortage of dentists in certain areas, using CNNs can lead to broader geographic coverage in detecting dental caries.
| S-EPMC10988262 | biostudies-literature