scholarly journals Identification and Diagnosis of Cerebral Stroke through Deep Convolutional Neural Network-Based Multimodal MRI Images

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Yanyan Pan ◽  
Huiping Zhang ◽  
Jinsuo Yang ◽  
Jing Guo ◽  
Zhiguo Yang ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Automatic Segmentation ◽  
Three Dimensional ◽  
Deep Convolutional Neural Network ◽  
Cerebral Stroke ◽  
Good Convergence ◽  
Segmentation Accuracy ◽  
Multimodal Mri ◽  
Magnetic Resonance Imaging Mri

This study aimed to explore the application value of multimodal magnetic resonance imaging (MRI) images based on the deep convolutional neural network (Conv.Net) in the diagnosis of strokes. Specifically, four automatic segmentation algorithms were proposed to segment multimodal MRI images of stroke patients. The segmentation effects were evaluated factoring into DICE, accuracy, sensitivity, and segmentation distance coefficient. It was found that although two-dimensional (2D) full convolutional neural network-based segmentation algorithm can locate and segment the lesion, its accuracy was low; the three-dimensional one exhibited higher accuracy, with various objective indicators improved, and the segmentation accuracy of the training set and the test set was 0.93 and 0.79, respectively, meeting the needs of automatic diagnosis. The asymmetric 3D residual U-Net network had good convergence and high segmentation accuracy, and the 3D deep residual network proposed on its basis had good segmentation coefficients, which can not only ensure segmentation accuracy but also avoid network degradation problems. In conclusion, the Conv.Net model can accurately segment the foci of patients with ischemic stroke and is suggested in clinic.

scholarly journals Development of in-house fully residual deep convolutional neural network-based segmentation software for the male pelvic CT

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Hideaki Hirashima ◽  
Mitsuhiro Nakamura ◽  
Pascal Baillehache ◽  
Yusuke Fujimoto ◽  
Shota Nakagawa ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Volumetric Modulated Arc Therapy ◽  
Intensity Modulated Radiotherapy ◽  
Deep Convolutional Neural Network ◽  
Training Dataset ◽  
Dice Similarity Coefficient ◽  
Optimal Model ◽  
Pelvic Region ◽  
Segmentation Accuracy

Abstract Background This study aimed to (1) develop a fully residual deep convolutional neural network (CNN)-based segmentation software for computed tomography image segmentation of the male pelvic region and (2) demonstrate its efficiency in the male pelvic region. Methods A total of 470 prostate cancer patients who had undergone intensity-modulated radiotherapy or volumetric-modulated arc therapy were enrolled. Our model was based on FusionNet, a fully residual deep CNN developed to semantically segment biological images. To develop the CNN-based segmentation software, 450 patients were randomly selected and separated into the training, validation and testing groups (270, 90, and 90 patients, respectively). In Experiment 1, to determine the optimal model, we first assessed the segmentation accuracy according to the size of the training dataset (90, 180, and 270 patients). In Experiment 2, the effect of varying the number of training labels on segmentation accuracy was evaluated. After determining the optimal model, in Experiment 3, the developed software was used on the remaining 20 datasets to assess the segmentation accuracy. The volumetric dice similarity coefficient (DSC) and the 95th-percentile Hausdorff distance (95%HD) were calculated to evaluate the segmentation accuracy for each organ in Experiment 3. Results In Experiment 1, the median DSC for the prostate were 0.61 for dataset 1 (90 patients), 0.86 for dataset 2 (180 patients), and 0.86 for dataset 3 (270 patients), respectively. The median DSCs for all the organs increased significantly when the number of training cases increased from 90 to 180 but did not improve upon further increase from 180 to 270. The number of labels applied during training had a little effect on the DSCs in Experiment 2. The optimal model was built by 270 patients and four organs. In Experiment 3, the median of the DSC and the 95%HD values were 0.82 and 3.23 mm for prostate; 0.71 and 3.82 mm for seminal vesicles; 0.89 and 2.65 mm for the rectum; 0.95 and 4.18 mm for the bladder, respectively. Conclusions We have developed a CNN-based segmentation software for the male pelvic region and demonstrated that the CNN-based segmentation software is efficient for the male pelvic region.

CT Image Segmentation of Liver Tumor with Deep Convolutional Neural Network

2021 ◽  
Vol 11 (2) ◽  
pp. 337-344
Author(s):  
Yao Zeng ◽  
Huanhuan Dai
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Automatic Segmentation ◽  
Abdominal Cavity ◽  
Mutual Exclusion ◽  
Image Data ◽  
Deep Convolutional Neural Network ◽  
Training Data ◽  
Segmentation Method ◽  
Segmentation Boundary

The liver is the largest substantial organ in the abdominal cavity of the human body. Its structure is complex, the incidence of vascular abundance is high, and it has been seriously ribbed, human health and life. In this study, an automatic segmentation method based on deep convolutional neural network is proposed. Image data blocks of different sizes are extracted as training data and different network structures are designed, and features are automatically learned to obtain a segmentation structure of the tumor. Secondly, in order to further refine the segmentation boundary, we establish a multi-region segmentation model with region mutual exclusion constraints. The model combines the image grayscale, gradient and prior probability information, and overcomes the problem that the boundary point attribution area caused by boundary blur and regional adhesion is difficult to determine. Finally, the model is solved quickly using the time-invisible multi-phase level set. Compared with the traditional multi-organ segmentation method, this method does not require registration or model initialization. The experimental results show that the model can segment the liver, kidney and spleen quickly and effectively, and the segmentation accuracy reaches the advanced level of current methods.

scholarly journals Combined Atlas and Convolutional Neural Network-Based Segmentation of the Hippocampus from MRI According to the ADNI Harmonized Protocol

Sensors ◽  
2021 ◽  
Vol 21 (7) ◽  
pp. 2427
Author(s):  
Samaneh Nobakht ◽  
Morgan Schaeffer ◽  
Nils Forkert ◽  
Sean Nestor ◽  
Sandra E. Black ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Neurological Diseases ◽  
Automatic Segmentation ◽  
Region Of Interest ◽  
Similarity Score ◽  
Segmentation Methods ◽  
Magnetic Resonance Imaging Mri ◽  
Hippocampus Segmentation ◽  
Better Than

Hippocampus atrophy is an early structural feature that can be measured from magnetic resonance imaging (MRI) to improve the diagnosis of neurological diseases. An accurate and robust standardized hippocampus segmentation method is required for reliable atrophy assessment. The aim of this work was to develop and evaluate an automatic segmentation tool (DeepHarp) for hippocampus delineation according to the ADNI harmonized hippocampal protocol (HarP). DeepHarp utilizes a two-step process. First, the approximate location of the hippocampus is identified in T1-weighted MRI datasets using an atlas-based approach, which is used to crop the images to a region-of-interest (ROI) containing the hippocampus. In the second step, a convolutional neural network trained using datasets with corresponding manual hippocampus annotations is used to segment the hippocampus from the cropped ROI. The proposed method was developed and validated using 107 datasets with manually segmented hippocampi according to the ADNI-HarP standard as well as 114 multi-center datasets of patients with Alzheimer’s disease, mild cognitive impairment, cerebrovascular disease, and healthy controls. Twenty-three independent datasets manually segmented according to the ADNI-HarP protocol were used for testing to assess the accuracy, while an independent test-retest dataset was used to assess precision. The proposed DeepHarp method achieved a mean Dice similarity score of 0.88, which was significantly better than four other established hippocampus segmentation methods used for comparison. At the same time, the proposed method also achieved a high test-retest precision (mean Dice score: 0.95). In conclusion, DeepHarp can automatically segment the hippocampus from T1-weighted MRI datasets according to the ADNI-HarP protocol with high accuracy and robustness, which can aid atrophy measurements in a variety of pathologies.

scholarly journals HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data

2019 ◽  
Vol 35 (21) ◽  
pp. 4222-4228 ◽  
Author(s):  
Tong Liu ◽  
Zheng Wang
Keyword(s):  
Neural Network ◽  
High Resolution ◽  
Convolutional Neural Network ◽  
Mammalian Cells ◽  
Three Dimensional ◽  
Correlation Coefficients ◽  
Cell Types ◽  
Deep Convolutional Neural Network ◽  
Computational Method ◽  
Supplementary Information

Abstract Motivation High-resolution Hi-C data are indispensable for the studies of three-dimensional (3D) genome organization at kilobase level. However, generating high-resolution Hi-C data (e.g. 5 kb) by conducting Hi-C experiments needs millions of mammalian cells, which may eventually generate billions of paired-end reads with a high sequencing cost. Therefore, it will be important and helpful if we can enhance the resolutions of Hi-C data by computational methods. Results We developed a new computational method named HiCNN that used a 54-layer very deep convolutional neural network to enhance the resolutions of Hi-C data. The network contains both global and local residual learning with multiple speedup techniques included resulting in fast convergence. We used mean squared errors and Pearson’s correlation coefficients between real high-resolution and computationally predicted high-resolution Hi-C data to evaluate the method. The evaluation results show that HiCNN consistently outperforms HiCPlus, the only existing tool in the literature, when training and testing data are extracted from the same cell type (i.e. GM12878) and from two different cell types in the same or different species (i.e. GM12878 as training with K562 as testing, and GM12878 as training with CH12-LX as testing). We further found that the HiCNN-enhanced high-resolution Hi-C data are more consistent with real experimental high-resolution Hi-C data than HiCPlus-enhanced data in terms of indicating statistically significant interactions. Moreover, HiCNN can efficiently enhance low-resolution Hi-C data, which eventually helps recover two chromatin loops that were confirmed by 3D-FISH. Availability and implementation HiCNN is freely available at http://dna.cs.miami.edu/HiCNN/. Supplementary information Supplementary data are available at Bioinformatics online.

Segmentation of Brain Magnetic Resonance Images using Deep Learning Classification and Multi-modal Composition

2020 ◽  
Vol 15 (2) ◽  
pp. 94-108
Author(s):  
R. Kala ◽  
P. Deepa
Keyword(s):  
Neural Network ◽  
Brain Tumor ◽  
Convolutional Neural Network ◽  
Input Image ◽  
Deep Convolutional Neural Network ◽  
Tumor Segmentation ◽  
Mr Images ◽  
Brain Tumor Segmentation ◽  
Spatial Consistency ◽  
Segmentation Accuracy

Background: Accurate detection of brain tumor and its severity is a challenging task in the medical field. So there is a need for developing brain tumor detecting algorithms and it is an emerging one for diagnosis, planning the treatment and outcome evaluation. Materials and Methods: Brain tumor segmentation method using deep learning classification and multi-modal composition has been developed using the deep convolutional neural networks. The different modalities of MRI such as T1, flair, T1C and T2 are given as input for the proposed method. The MR images from the different modalities are used in proportion to the information contents in the particular modality. The weights for the different modalities are calculated blockwise and the standard deviation of the block is taken as a proxy for the information content of the block. Then the convolution is performed between the input image of the T1, flair, T1C and T2 MR images and corresponding to the weight of the T1, flair, T1C, and T2 images. The convolution is summed between the different modalities of the MR images and its corresponding weight of the different modalities of the MR images to obtain a new composite image which is given as an input image to the deep convolutional neural network. The deep convolutional neural network performs segmentation through the different layers of CNN and different filter operations are performed in each layer to obtain the enhanced classification and segmented spatial consistency results. The analysis of the proposed method shows that the discriminatory information from the different modalities is effectively combined to increase the overall accuracy of segmentation. Results: The proposed deep convolutional neural network for brain tumor segmentation method has been analysed by using the Brain Tumor Segmentation Challenge 2013 database (BRATS 2013). The complete, core and enhancing regions are validated with Dice Similarity Coefficient and Jaccard similarity index metric for the Challenge, Leaderboard, and Synthetic data set. To evaluate the classification rates, the metrics such as accuracy, precision, sensitivity, specificity, under-segmentation, incorrect segmentation and over segmentation also evaluated and compared with the existing methods. Experimental results exhibit a higher degree of precision in the segmentation compared to existing methods. Conclusion: In this work, deep convolution neural network with different modalities of MR image are used to detect the brain tumor. The new input image was created by convoluting the input image of the different modalities and their weights. The weights are determined using the standard deviation of the block. Segmentation accuracy is high with efficient appearance and spatial consistency. The assessment of segmented images is completely evaluated by using well-established metrics. In future, the proposed method will be considered and evaluated with other databases and the segmentation accuracy results should be analysed with the presence of different kind of noises.

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