scholarly journals Deep-Learning-Based Accelerated and Noise-Suppressed Estimation (DANSE) of quantitative Gradient Recalled Echo (qGRE) MRI metrics associated with Human Brain Neuronal Structure and Hemodynamic Properties

2021 ◽  
Author(s):  
Sayan Kahali ◽  
Satya V.V.N. Kothapalli ◽  
Xiaojian Xu ◽  
Ulugbek S Kamilov ◽  
Dmitriy A Yablonskiy
Keyword(s):  
Magnetic Field ◽  
Deep Learning ◽  
Noise Suppression ◽  
Ground Truth ◽  
Least Square ◽  
Biophysical Model ◽  
Neuronal Structure ◽  
Brain Maps ◽  
Computational Speed ◽  
Phase Images

Purpose: To introduce a Deep-Learning-Based Accelerated and Noise-Suppressed Estimation (DANSE) method for reconstructing quantitative maps of biological tissue cellular-specific, and hemodynamic-specific, from Gradient-Recalled-Echo (GRE) MRI data with multiple gradient-recalled echoes. Methods: DANSE method adapts supervised learning paradigm to train a convolutional neural network for robust estimation of and maps free from the adverse effects of macroscopic (B0) magnetic field inhomogeneities directly from the GRE magnitude images without utilizing phase images. The corresponding ground-truth maps were generated by means of a voxel-by-voxel fitting of a previously-developed biophysical quantitative GRE (qGRE) model accounting for tissue, hemodynamic and -inhomogeneities contributions to GRE signal with multiple gradient echoes using nonlinear least square (NLLS) algorithm. Results: We show that the DANSE model efficiently estimates the aforementioned brain maps and preserves all features of NLLS approach with significant improvements including noise-suppression and computation speed (from many hours to seconds). The noise-suppression feature of DANSE is especially prominent for data with SNR characteristic for typical GRE data (SNR~50), where DANSE-generated and maps had three times smaller errors than that of NLLS method. Conclusions: DANSE method enables fast reconstruction of magnetic-field-inhomogeneity-free and noise-suppressed quantitative qGRE brain maps. DANSE method does not require any information about field inhomogeneities during application. It exploits spatial patterns in the qGRE MRI data and previously-gained knowledge from the biophysical model, thus producing clean brain maps even in the environments with high noise levels. These features along with fast computational speed can lead to broad qGRE clinical and research applications.

scholarly journals Phasetime: Deep Learning Approach to Detect Nuclei in Time Lapse Phase Images

2019 ◽  
Vol 8 (8) ◽  
pp. 1159 ◽  
Author(s):  
Pengyu Yuan ◽  
Ali Rezvan ◽  
Xiaoyang Li ◽  
Navin Varadarajan ◽  
Hien Van Nguyen
Keyword(s):  
Deep Learning ◽  
Ground Truth ◽  
Time Lapse ◽  
Phase Image ◽  
Training Time ◽  
Blob Detection ◽  
Phase Images ◽  
The Mean ◽  
Fluorescent Tags ◽  
Time Lapse Imaging

Time lapse microscopy is essential for quantifying the dynamics of cells, subcellular organelles and biomolecules. Biologists use different fluorescent tags to label and track the subcellular structures and biomolecules within cells. However, not all of them are compatible with time lapse imaging, and the labeling itself can perturb the cells in undesirable ways. We hypothesized that phase image has the requisite information to identify and track nuclei within cells. By utilizing both traditional blob detection to generate binary mask labels from the stained channel images and the deep learning Mask RCNN model to train a detection and segmentation model, we managed to segment nuclei based only on phase images. The detection average precision is 0.82 when the IoU threshold is to be set 0.5. And the mean IoU for masks generated from phase images and ground truth masks from experts is 0.735. Without any ground truth mask labels during the training time, this is good enough to prove our hypothesis. This result enables the ability to detect nuclei without the need for exogenous labeling.

scholarly journals Spectroscopic and deep learning-based approaches to identify and quantify cerebral microhemorrhages

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Crouzet ◽  
Gwangjin Jeong ◽  
Rachel H. Chae ◽  
Krystal T. LoPresti ◽  
Cody E. Dunn ◽  
...  
Keyword(s):  
Deep Learning ◽  
Prussian Blue ◽  
Processing Speed ◽  
Digital Pathology ◽  
Ground Truth ◽  
Individual Variability ◽  
Rgb Images ◽  
Cerebral Microhemorrhages ◽  
Phasor Analysis ◽  
Better Than

AbstractCerebral microhemorrhages (CMHs) are associated with cerebrovascular disease, cognitive impairment, and normal aging. One method to study CMHs is to analyze histological sections (5–40 μm) stained with Prussian blue. Currently, users manually and subjectively identify and quantify Prussian blue-stained regions of interest, which is prone to inter-individual variability and can lead to significant delays in data analysis. To improve this labor-intensive process, we developed and compared three digital pathology approaches to identify and quantify CMHs from Prussian blue-stained brain sections: (1) ratiometric analysis of RGB pixel values, (2) phasor analysis of RGB images, and (3) deep learning using a mask region-based convolutional neural network. We applied these approaches to a preclinical mouse model of inflammation-induced CMHs. One-hundred CMHs were imaged using a 20 × objective and RGB color camera. To determine the ground truth, four users independently annotated Prussian blue-labeled CMHs. The deep learning and ratiometric approaches performed better than the phasor analysis approach compared to the ground truth. The deep learning approach had the most precision of the three methods. The ratiometric approach has the most versatility and maintained accuracy, albeit with less precision. Our data suggest that implementing these methods to analyze CMH images can drastically increase the processing speed while maintaining precision and accuracy.

scholarly journals Matching Large Baseline Oblique Stereo Images Using an End-to-End Convolutional Neural Network

2021 ◽  
Vol 13 (2) ◽  
pp. 274
Author(s):  
Guobiao Yao ◽  
Alper Yilmaz ◽  
Li Zhang ◽  
Fei Meng ◽  
Haibin Ai ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Stereo Matching ◽  
Least Square ◽  
Affine Invariant ◽  
Stereo Images ◽  
Distance Ratio ◽  
Matching Algorithm ◽  
End To End

The available stereo matching algorithms produce large number of false positive matches or only produce a few true-positives across oblique stereo images with large baseline. This undesired result happens due to the complex perspective deformation and radiometric distortion across the images. To address this problem, we propose a novel affine invariant feature matching algorithm with subpixel accuracy based on an end-to-end convolutional neural network (CNN). In our method, we adopt and modify a Hessian affine network, which we refer to as IHesAffNet, to obtain affine invariant Hessian regions using deep learning framework. To improve the correlation between corresponding features, we introduce an empirical weighted loss function (EWLF) based on the negative samples using K nearest neighbors, and then generate deep learning-based descriptors with high discrimination that is realized with our multiple hard network structure (MTHardNets). Following this step, the conjugate features are produced by using the Euclidean distance ratio as the matching metric, and the accuracy of matches are optimized through the deep learning transform based least square matching (DLT-LSM). Finally, experiments on Large baseline oblique stereo images acquired by ground close-range and unmanned aerial vehicle (UAV) verify the effectiveness of the proposed approach, and comprehensive comparisons demonstrate that our matching algorithm outperforms the state-of-art methods in terms of accuracy, distribution and correct ratio. The main contributions of this article are: (i) our proposed MTHardNets can generate high quality descriptors; and (ii) the IHesAffNet can produce substantial affine invariant corresponding features with reliable transform parameters.

scholarly journals IMG-22. A DEEP LEARNING MODEL FOR AUTOMATIC POSTERIOR FOSSA PEDIATRIC BRAIN TUMOR SEGMENTATION: A MULTI-INSTITUTIONAL STUDY

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii359-iii359
Author(s):  
Lydia Tam ◽  
Edward Lee ◽  
Michelle Han ◽  
Jason Wright ◽  
Leo Chen ◽  
...  
Keyword(s):  
Deep Learning ◽  
Posterior Fossa ◽  
Ground Truth ◽  
Learning Model ◽  
Tumor Segmentation ◽  
Dice Similarity Coefficient ◽  
Study Cohort ◽  
Navigation Systems ◽  
Tumor Types ◽  
Deep Learning Model

Abstract BACKGROUND Brain tumors are the most common solid malignancies in childhood, many of which develop in the posterior fossa (PF). Manual tumor measurements are frequently required to optimize registration into surgical navigation systems or for surveillance of nonresectable tumors after therapy. With recent advances in artificial intelligence (AI), automated MRI-based tumor segmentation is now feasible without requiring manual measurements. Our goal was to create a deep learning model for automated PF tumor segmentation that can register into navigation systems and provide volume output. METHODS 720 pre-surgical MRI scans from five pediatric centers were divided into training, validation, and testing datasets. The study cohort comprised of four PF tumor types: medulloblastoma, diffuse midline glioma, ependymoma, and brainstem or cerebellar pilocytic astrocytoma. Manual segmentation of the tumors by an attending neuroradiologist served as “ground truth” labels for model training and evaluation. We used 2D Unet, an encoder-decoder convolutional neural network architecture, with a pre-trained ResNet50 encoder. We assessed ventricle segmentation accuracy on a held-out test set using Dice similarity coefficient (0–1) and compared ventricular volume calculation between manual and model-derived segmentations using linear regression. RESULTS Compared to the ground truth expert human segmentation, overall Dice score for model performance accuracy was 0.83 for automatic delineation of the 4 tumor types. CONCLUSIONS In this multi-institutional study, we present a deep learning algorithm that automatically delineates PF tumors and outputs volumetric information. Our results demonstrate applied AI that is clinically applicable, potentially augmenting radiologists, neuro-oncologists, and neurosurgeons for tumor evaluation, surveillance, and surgical planning.

scholarly journals Neural Network for Metal Detection Based on Magnetic Impedance Sensor

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4456
Author(s):  
Sungjae Ha ◽  
Dongwoo Lee ◽  
Hoijun Kim ◽  
Soonchul Kwon ◽  
EungJo Kim ◽  
...  
Keyword(s):  
Neural Network ◽  
Magnetic Field ◽  
Deep Learning ◽  
Short Term Memory ◽  
Magnetic Impedance ◽  
Detection Technology ◽  
Metal Detection ◽  
Long Short Term Memory ◽  
Impedance Sensor ◽  
The Magnetic Field

The efficiency of the metal detection method using deep learning with data obtained from multiple magnetic impedance (MI) sensors was investigated. The MI sensor is a passive sensor that detects metal objects and magnetic field changes. However, when detecting a metal object, the amount of change in the magnetic field caused by the metal is small and unstable with noise. Consequently, there is a limit to the detectable distance. To effectively detect and analyze this distance, a method using deep learning was applied. The detection performances of a convolutional neural network (CNN) and a recurrent neural network (RNN) were compared from the data extracted from a self-impedance sensor. The RNN model showed better performance than the CNN model. However, in the shallow stage, the CNN model was superior compared to the RNN model. The performance of a deep-learning-based (DLB) metal detection network using multiple MI sensors was compared and analyzed. The network was detected using long short-term memory and CNN. The performance was compared according to the number of layers and the size of the metal sheet. The results are expected to contribute to sensor-based DLB detection technology.

Patch-CNN: Deep learning for logo detection and brand recognition

2021 ◽  
pp. 1-14
Author(s):  
Waqas Yousaf ◽  
Arif Umar ◽  
Syed Hamad Shirazi ◽  
Zakir Khan ◽  
Imran Razzak ◽  
...  
Keyword(s):  
Deep Learning ◽  
Image Quality ◽  
Ground Truth ◽  
Logo Recognition ◽  
Brand Recognition ◽  
Detection And Recognition

Automatic logo detection and recognition is significantly growing due to the increasing requirements of intelligent documents analysis and retrieval. The main problem to logo detection is intra-class variation, which is generated by the variation in image quality and degradation. The problem of misclassification also occurs while having tiny logo in large image with other objects. To address this problem, Patch-CNN is proposed for logo recognition which uses small patches of logos for training to solve the problem of misclassification. The classification is accomplished by dividing the logo images into small patches and threshold is applied to drop no logo area according to ground truth. The architectures of AlexNet and ResNet are also used for logo detection. We propose a segmentation free architecture for the logo detection and recognition. In literature, the concept of region proposal generation is used to solve logo detection, but these techniques suffer in case of tiny logos. Proposed CNN is especially designed for extracting the detailed features from logo patches. So far, the technique has attained accuracy equals to 0.9901 with acceptable training and testing loss on the dataset used in this work.

scholarly journals Deep Learning Based Cardiac MRI Segmentation: Do We Need Experts?

Algorithms ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 212
Author(s):  
Youssef Skandarani ◽  
Pierre-Marc Jodoin ◽  
Alain Lalande
Keyword(s):  
Deep Learning ◽  
Cardiac Mri ◽  
Expert Knowledge ◽  
Medical Image Analysis ◽  
Ground Truth ◽  
Cine Mri ◽  
Data Sets ◽  
Mri Segmentation ◽  
Segmentation Evaluation ◽  
Ground Truth Data

Deep learning methods are the de facto solutions to a multitude of medical image analysis tasks. Cardiac MRI segmentation is one such application, which, like many others, requires a large number of annotated data so that a trained network can generalize well. Unfortunately, the process of having a large number of manually curated images by medical experts is both slow and utterly expensive. In this paper, we set out to explore whether expert knowledge is a strict requirement for the creation of annotated data sets on which machine learning can successfully be trained. To do so, we gauged the performance of three segmentation models, namely U-Net, Attention U-Net, and ENet, trained with different loss functions on expert and non-expert ground truth for cardiac cine–MRI segmentation. Evaluation was done with classic segmentation metrics (Dice index and Hausdorff distance) as well as clinical measurements, such as the ventricular ejection fractions and the myocardial mass. The results reveal that generalization performances of a segmentation neural network trained on non-expert ground truth data is, to all practical purposes, as good as that trained on expert ground truth data, particularly when the non-expert receives a decent level of training, highlighting an opportunity for the efficient and cost-effective creation of annotations for cardiac data sets.

A Least Square Method for Measurement and Optimisation in Selected Physical Experiments

2005 ◽  
Vol 295-296 ◽  
pp. 681-686 ◽  
Author(s):  
I. Frollo ◽  
P. Andris ◽  
I. Strolka ◽  
L. Bačiak
Keyword(s):  
Magnetic Field ◽  
Input Parameter ◽  
Target Function ◽  
Least Square Method ◽  
Least Square ◽  
Physical Experiments ◽  
Magnetic Field Homogeneity ◽  
Field Homogeneity ◽  
Basic Parameters ◽  
Shim Coils

The scope of this paper is to demonstrate a least square method for optimisation of basic parameters for selected physical experiment design where large input parameter measurement and adjustment is needed. The speed of calculation and experimentally verified results are promising to use this method in many physical projects. We have demonstrated this method for computation of feeding currents of correcting coils for stationary magnetic field used in NMR imaging. A set of linear equation definition and determination of a target function and optimisation computations are presented with procedures that provide optimal values of currents for shim coils. The proposed method, because of its simplicity and speed of computation, is convenient for basic adjustment of the magnetic field homogeneity by the first magnet installation. It is also suitable for periodic testing and magnet inhomogeneity correction for MRI magnets.

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