A Semiautomated Deep Learning Approach for Pancreas Segmentation.
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ABSTRACT:
SUBMITTER: Huang M
PROVIDER: S-EPMC8272661 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:PurposeThis study focuses on assessing the performance of active learning techniques to train a brain MRI glioma segmentation model.MethodsThe publicly available training dataset provided for the 2021 RSNA-ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge was used in this study, consisting of 1251 multi-institutional, multi-parametric MR images. Post-contrast T1, T2, and T2 FLAIR images as well as ground truth manual segmentation were used as input for the model. The data were split into a training set of 1151 cases and testing set of 100 cases, with the testing set remaining constant throughout. Deep convolutional neural network segmentation models were trained using the NiftyNet platform. To test the viability of active learning in training a segmentation model, an initial reference model was trained using all 1151 training cases followed by two additional models using only 575 cases and 100 cases. The resulting predicted segmentations of these two additional models on the remaining training cases were then addended to the training dataset for additional training.ResultsIt was demonstrated that an active learning approach for manual segmentation can lead to comparable model performance for segmentation of brain gliomas (0.906 reference Dice score vs 0.868 active learning Dice score) while only requiring manual annotation for 28.6% of the data.ConclusionThe active learning approach when applied to model training can drastically reduce the time and labor spent on preparation of ground truth training data.Critical relevance statementActive learning concepts were applied to a deep learning-assisted segmentation of brain gliomas from MR images to assess their viability in reducing the required amount of manually annotated ground truth data in model training.Key points• This study focuses on assessing the performance of active learning techniques to train a brain MRI glioma segmentation model. • The active learning approach for manual segmentation can lead to comparable model performance for segmentation of brain gliomas. • Active learning when applied to model training can drastically reduce the time and labor spent on preparation of ground truth training data.
| S-EPMC10449747 | biostudies-literature
Project description:Malaria is an endemic life-threating disease caused by the unicellular protozoan parasites of the genus Plasmodium. Confirming the presence of parasites early in all malaria cases ensures species-specific antimalarial treatment, reducing the mortality rate, and points to other illnesses in negative cases. However, the gold standard remains the light microscopy of May-Grünwald-Giemsa (MGG)-stained thin and thick peripheral blood (PB) films. This is a time-consuming procedure, dependent on a pathologist's skills, meaning that healthcare providers may encounter difficulty in diagnosing malaria in places where it is not endemic. This work presents a novel three-stage pipeline to (1) segment erythrocytes, (2) crop and mask them, and (3) classify them into malaria infected or not. The first and third steps involved the design, training, validation and testing of a Segmentation Neural Network and a Convolutional Neural Network from scratch using a Graphic Processing Unit. Segmentation achieved a global accuracy of 93.72% over the test set and the specificity for malaria detection in red blood cells (RBCs) was 87.04%. This work shows the potential that deep learning has in the digital pathology field and opens the way for future improvements, as well as for broadening the use of the created networks.
| S-EPMC7517192 | biostudies-literature
Project description:A pressure ulcer is an injury of the skin and underlying tissues adjacent to a bony eminence. Patients who suffer from this disease may have difficulty accessing medical care. Recently, the COVID-19 pandemic has exacerbated this situation. Automatic diagnosis based on machine learning (ML) brings promising solutions. Traditional ML requires complicated preprocessing steps for feature extraction. Its clinical applications are thus limited to particular datasets. Deep learning (DL), which extracts features from convolution layers, can embrace larger datasets that might be deliberately excluded in traditional algorithms. However, DL requires large sets of domain specific labeled data for training. Labeling various tissues of pressure ulcers is a challenge even for experienced plastic surgeons. We propose a superpixel-assisted, region-based method of labeling images for tissue classification. The boundary-based method is applied to create a dataset for wound and re-epithelialization (re-ep) segmentation. Five popular DL models (U-Net, DeeplabV3, PsPNet, FPN, and Mask R-CNN) with encoder (ResNet-101) were trained on the two datasets. A total of 2836 images of pressure ulcers were labeled for tissue classification, while 2893 images were labeled for wound and re-ep segmentation. All five models had satisfactory results. DeeplabV3 had the best performance on both tasks with a precision of 0.9915, recall of 0.9915 and accuracy of 0.9957 on the tissue classification; and a precision of 0.9888, recall of 0.9887 and accuracy of 0.9925 on the wound and re-ep segmentation task. Combining segmentation results with clinical data, our algorithm can detect the signs of wound healing, monitor the progress of healing, estimate the wound size, and suggest the need for surgical debridement.
| S-EPMC8853507 | biostudies-literature
Project description:Engineered RNA elements are programmable tools capable of detecting small molecules, proteins, and nucleic acids. Predicting the behavior of these tools remains a challenge, a situation that could be addressed through enhanced pattern recognition from deep learning. Thus, we investigate Deep Neural Networks (DNN) to predict toehold switch function as a canonical riboswitch model in synthetic biology. To facilitate DNN training, we synthesized and characterized in vivo a dataset of 91,534 toehold switches spanning 23 viral genomes and 906 human transcription factors. DNNs trained on nucleotide sequences outperformed (R2=0.43-0.70) previous state-of-the-art thermodynamic and kinetic models (R2=0.04-0.15) and allowed for human-understandable attention-visualizations (VIS4Map) to identify success and failure modes. This deep learning approach constitutes a major step forward in engineering and understanding of RNA synthetic biology.
2020-08-12 | GSE149225 | GEO
Project description:Deep learning is rapidly becoming the technique of choice for automated segmentation of nuclei in biological image analysis workflows. In order to evaluate the feasibility of training nuclear segmentation models on small, custom annotated image datasets that have been augmented, we have designed a computational pipeline to systematically compare different nuclear segmentation model architectures and model training strategies. Using this approach, we demonstrate that transfer learning and tuning of training parameters, such as the composition, size, and preprocessing of the training image dataset, can lead to robust nuclear segmentation models, which match, and often exceed, the performance of existing, off-the-shelf deep learning models pretrained on large image datasets. We envision a practical scenario where deep learning nuclear segmentation models trained in this way can be shared across a laboratory, facility, or institution, and continuously improved by training them on progressively larger and varied image datasets. Our work provides computational tools and a practical framework for deep learning-based biological image segmentation using small annotated image datasets. Published [2020]. This article is a U.S. Government work and is in the public domain in the USA.
| S-EPMC8914348 | biostudies-literature
Project description:The purpose of this study was to introduce a new deep learning (DL) model for segmentation of the fovea avascular zone (FAZ) in en face optical coherence tomography angiography (OCTA) and compare the results with those of the device's built-in software and manual measurements in healthy subjects and diabetic patients. In this retrospective study, FAZ borders were delineated in the inner retinal slab of 3 × 3 enface OCTA images of 131 eyes of 88 diabetic patients and 32 eyes of 18 healthy subjects. To train a deep convolutional neural network (CNN) model, 126 enface OCTA images (104 eyes with diabetic retinopathy and 22 normal eyes) were used as training/validation dataset. Then, the accuracy of the model was evaluated using a dataset consisting of OCTA images of 10 normal eyes and 27 eyes with diabetic retinopathy. The CNN model was based on Detectron2, an open-source modular object detection library. In addition, automated FAZ measurements were conducted using the device's built-in commercial software, and manual FAZ delineation was performed using ImageJ software. Bland-Altman analysis was used to show 95% limit of agreement (95% LoA) between different methods. The mean dice similarity coefficient of the DL model was 0.94 ± 0.04 in the testing dataset. There was excellent agreement between automated, DL model and manual measurements of FAZ in healthy subjects (95% LoA of - 0.005 to 0.026 mm2 between automated and manual measurement and 0.000 to 0.009 mm2 between DL and manual FAZ area). In diabetic eyes, the agreement between DL and manual measurements was excellent (95% LoA of - 0.063 to 0.095), however, there was a poor agreement between the automated and manual method (95% LoA of - 0.186 to 0.331). The presence of diabetic macular edema and intraretinal cysts at the fovea were associated with erroneous FAZ measurements by the device's built-in software. In conclusion, the DL model showed an excellent accuracy in detection of FAZ border in enfaces OCTA images of both diabetic patients and healthy subjects. The DL and manual measurements outperformed the automated measurements of the built-in software.
| S-EPMC7806603 | biostudies-literature
Project description:ObjectiveRadiomic and deep learning studies based on magnetic resonance imaging (MRI) of liver tumor are gradually increasing. Manual segmentation of normal hepatic tissue and tumor exhibits limitations.Methods105 patients diagnosed with hepatocellular carcinoma were retrospectively studied between Jan 2015 and Dec 2020. The patients were divided into three sets: training (n = 83), validation (n = 11), and internal testing (n = 11). Additionally, 9 cases were included from the Cancer Imaging Archive as the external test set. Using the arterial phase and T2WI sequences, expert radiologists manually delineated all images. Using deep learning, liver tumors and liver segments were automatically segmented. A preliminary liver segmentation was performed using the UNet + + network, and the segmented liver mask was re-input as the input end into the UNet + + network to segment liver tumors. The false positivity rate was reduced using a threshold value in the liver tumor segmentation. To evaluate the segmentation results, we calculated the Dice similarity coefficient (DSC), average false positivity rate (AFPR), and delineation time.ResultsThe average DSC of the liver in the validation and internal testing sets was 0.91 and 0.92, respectively. In the validation set, manual and automatic delineation took 182.9 and 2.2 s, respectively. On an average, manual and automatic delineation took 169.8 and 1.7 s, respectively. The average DSC of liver tumors was 0.612 and 0.687 in the validation and internal testing sets, respectively. The average time for manual and automatic delineation and AFPR in the internal testing set were 47.4 s, 2.9 s, and 1.4, respectively, and those in the external test set were 29.5 s, 4.2 s, and 1.6, respectively.ConclusionUNet + + can automatically segment normal hepatic tissue and liver tumors based on MR images. It provides a methodological basis for the automated segmentation of liver tumors, improves the delineation efficiency, and meets the requirement of extraction set analysis of further radiomics and deep learning.
| S-EPMC10623778 | biostudies-literature
Project description:Stereotactic radiosurgery planning for cerebral arteriovenous malformations (AVM) is complicated by the variability in appearance of an AVM nidus across different imaging modalities. We developed a deep learning approach to automatically segment cerebrovascular-anatomical maps from multiple high-resolution magnetic resonance imaging/angiography (MRI/MRA) sequences in AVM patients, with the goal of facilitating target delineation. Twenty-three AVM patients who were evaluated for radiosurgery and underwent multi-parametric MRI/MRA were included. A hybrid semi-automated and manual approach was used to label MRI/MRAs with arteries, veins, brain parenchyma, cerebral spinal fluid (CSF), and embolized vessels. Next, these labels were used to train a convolutional neural network to perform this task. Imaging from 17 patients (6362 image slices) was used for training, and 6 patients (1224 slices) for validation. Performance was evaluated by Dice Similarity Coefficient (DSC). Classification performance was good for arteries, veins, brain parenchyma, and CSF, with DSCs of 0.86, 0.91, 0.98, and 0.91, respectively in the validation image set. Performance was lower for embolized vessels, with a DSC of 0.75. This demonstrates the proof of principle that accurate, high-resolution cerebrovascular-anatomical maps can be generated from multiparametric MRI/MRA. Clinical validation of their utility in radiosurgery planning is warranted.
| S-EPMC8763944 | biostudies-literature
Project description:The detection of contrast-enhancing lesions (CELs) is fundamental for the diagnosis and monitoring of patients with multiple sclerosis (MS). This task is time-consuming and suffers from high intra- and inter-rater variability in clinical practice. However, only a few studies proposed automatic approaches for CEL detection. This study aimed to develop a deep learning model that automatically detects and segments CELs in clinical Magnetic Resonance Imaging (MRI) scans. A 3D UNet-based network was trained with clinical MRI from the Swiss Multiple Sclerosis Cohort. The dataset comprised 372 scans from 280 MS patients: 162 showed at least one CEL, while 118 showed no CELs. The input dataset consisted of T1-weighted before and after gadolinium injection, and FLuid Attenuated Inversion Recovery images. The sampling strategy was based on a white matter lesion mask to confirm the existence of real contrast-enhancing lesions. To overcome the dataset imbalance, a weighted loss function was implemented. The Dice Score Coefficient and True Positive and False Positive Rates were 0.76, 0.93, and 0.02, respectively. Based on these results, the model developed in this study might well be considered for clinical decision support.
| S-EPMC11351944 | biostudies-literature
Project description:One of the main requirements of tumor extraction is the annotation and segmentation of tumor boundaries correctly. For this purpose, we present a threefold deep learning architecture. First, classifiers are implemented with a deep convolutional neural network (CNN) and second a region-based convolutional neural network (R-CNN) is performed on the classified images to localize the tumor regions of interest. As the third and final stage, the concentrated tumor boundary is contoured for the segmentation process by using the Chan-Vese segmentation algorithm. As the typical edge detection algorithms based on gradients of pixel intensity tend to fail in the medical image segmentation process, an active contour algorithm defined with the level set function is proposed. Specifically, the Chan-Vese algorithm was applied to detect the tumor boundaries for the segmentation process. To evaluate the performance of the overall system, Dice Score, Rand Index (RI), Variation of Information (VOI), Global Consistency Error (GCE), Boundary Displacement Error (BDE), Mean Absolute Error (MAE), and Peak Signal to Noise Ratio (PSNR) were calculated by comparing the segmented boundary area which is the final output of the proposed, against the demarcations of the subject specialists which is the gold standard. Overall performance of the proposed architecture for both glioma and meningioma segmentation is with an average Dice Score of 0.92 (also, with RI of 0.9936, VOI of 0.0301, GCE of 0.004, BDE of 2.099, PSNR of 77.076, and MAE of 52.946), pointing to the high reliability of the proposed architecture.
| S-EPMC7948532 | biostudies-literature