با سلام خدمت کاربران عزیز، به اطلاع می رساند ترجمه مقالاتی که سال انتشار آن ها زیر 2008 می باشد رایگان بوده و میتوانید با وارد شدن در صفحه جزییات مقاله به رایگان ترجمه را دانلود نمایید.
MISS-D: A fast and scalable framework of medical image storage service based on distributed file system
MISS-D: یک چارچوب سریع و مقیاس پذیر از خدمات ذخیره سازی تصویر پزشکی بر اساس سیستم فایل توزیع شده-2020
Background and Objective Processing of medical imaging big data is deeply challenging due to the size of data, computational complexity, security storage and inherent privacy issues. Traditional picture archiving and communication system, which is an imaging technology used in the healthcare industry, generally uses centralized high performance disk storage arrays in the practical solutions. The existing storage solutions are not suitable for the diverse range of medical imaging big data that needs to be stored reliably and accessed in a timely manner. The economical solution is emerging as the cloud computing which provides scalability, elasticity, performance and better managing cost. Cloud based storage architecture for medical imaging big data has attracted more and more attention in industry and academia. Methods This study presents a novel, fast and scalable framework of medical image storage service based on distributed file system. Two innovations of the framework are introduced in this paper. An integrated medical imaging content indexing file model for large-scale image sequence is designed to adapt to the high performance storage efficiency on distributed file system. A virtual file pooling technology is proposed, which uses the memory-mapped file method to achieve an efficient data reading process and provides the data swapping strategy in the pool. Result The experiments show that the framework not only has comparable performance of reading and writing files which meets requirements in real-time application domain, but also bings greater convenience for clinical system developers by multiple client accessing types. The framework supports different user client types through the unified micro-service interfaces which basically meet the needs of clinical system development especially for online applications. The experimental results demonstrate the framework can meet the needs of real-time data access as well as traditional picture archiving and communication system. Conclusions This framework aims to allow rapid data accessing for massive medical images, which can be demonstrated by the online web client for MISS-D framework implemented in this paper for real-time data interaction. The framework also provides a substantial subset of features to existing open-source and commercial alternatives, which has a wide range of potential applications.
Keywords: Hadoop distributed file system | Data packing | Memory mapping file | Message queue | Micro-service | Medical imaging
STrategically Acquired Gradient Echo (STAGE) imaging, part III: Technical advances and clinical applications of a rapid multi-contrast multi-parametric brain imaging method
تصویربرداری گرادیان اکو (STAGE) استراتژیک ، بخش سوم: پیشرفت های فنی و برنامه های بالینی از یک روش تصویربرداری سریع مغزی چند پارامتری سریع با کنتراست-2020
One major thrust in radiology today is image standardization with a focus on rapidly acquired quantitative multi-contrast information. This is critical for multi-center trials, for the collection of big data and for the use of artificial intelligence in evaluating the data. Strategically acquired gradient echo (STAGE) imaging is one such method that can provide 8 qualitative and 7 quantitative pieces of information in 5 min or less at 3 T. STAGE provides qualitative images in the form of proton density weighted images, T1 weighted images, T2* weighted images and simulated double inversion recovery (DIR) images. STAGE also provides quantitative data in the form of proton spin density, T1, T2* and susceptibility maps as well as segmentation of white matter, gray matter and cerebrospinal fluid. STAGE uses vendors product gradient echo sequences. It can be applied from 0.35 T to 7 T across all manufacturers producing similar results in contrast and quantification of the data. In this paper, we discuss the strengths and weaknesses of STAGE, demonstrate its contrast-to-noise (CNR) behavior relative to a large clinical data set and introduce a few new image contrasts derived from STAGE, including DIR images and a new concept referred to as true susceptibility weighted imaging (tSWI) linked to fluid attenuated inversion recovery (FLAIR) or tSWI-FLAIR for the evaluation of multiple sclerosis lesions. The robustness of STAGE T1 mapping was tested using the NIST/NIH phantom, while the reproducibility was tested by scanning a given individual ten times in one session and the same subject scanned once a week over a 12-week period. Assessment of the CNR for the enhanced T1W image (T1WE) showed a significantly better contrast between gray matter and white matter than conventional T1W images in both patients with Parkinsons disease and healthy controls. We also present some clinical cases using STAGE imaging in patients with stroke, metastasis, multiple sclerosis and a fetus with ventriculomegaly. Overall, STAGE is a comprehensive protocol that provides the clinician with numerous qualitative and quantitative images.
Keywords: Quantitative magnetic resonance imaging | Susceptibility weighted imaging | T1 mapping | Quantitative susceptibility mapping | Multi-parametric magnetic resonance imaging | Strategically acquired gradient echo
Log-sum enhanced sparse deep neural network
شبکه عصبی پراکنده عمیق با افزایش log-sum-2020
How to design deep neural networks (DNNs) for the representation and analysis of high dimensional but small sample size data is still a big challenge. One solution is to construct a sparse network. At present, there exist many approaches to achieve sparsity for DNNs by regularization, but most of them are carried out only in the pre-training process due to the difficulty in the derivation of explicit formulae in the finetuning process. In this paper, a log-sum function is used as the regularization terms for both the responses of hidden neurons and the network connections in the loss function of the fine-tuning process. It provides a better approximation to the L0-norm than several often used norms. Based on the gradient formula of the loss function, the fine-tuning process can be executed more efficiently. Specifically, the commonly used gradient calculation in many deep learning research platforms, such as PyTorch or TensorFlow, can be accelerated. Given the analytic formula for calculating gradients used in any layer of DNN, the error accumulated from successive numerical approximations in the differentiation process can be avoided. With the proposed log-sum enhanced sparse deep neural network (LSES-DNN), the sparsity of the responses and the connections can be well controlled to improve the adaptivity of DNNs. The proposed model is applied to MRI data for both the diagnosis of schizophrenia and the study of brain developments. Numerical experiments demonstrate its superior performance among several classical classifiers tested.
Keywords: Deep neural network | Log-sum enhanced sparsity | Back propagation algorithm | Concise gradient formula | Magnetic resonance imaging
Discovering the shared biology of cognitive traits determined by genetic overlap
کشف زیست شناسی مشترک صفات شناختی که با همپوشانی ژنتیکی تعیین می شوند-2020
Investigating the contribution of biology to human cognition has assumed a bottom-up causal cascade where genes influence brain systems that activate, communicate, and ultimately drive behavior. Yet few studies have directly tested whether cognitive traits with overlapping genetic underpinnings also rely on overlapping brain systems. Here, we report a step-wise exploratory analysis of genetic and functional imaging overlaps among cognitive traits. We used twin-based genetic analyses in the human connectome project (HCP) dataset (N ¼ 486), in which we quantified the heritability of measures of cognitive functions, and tested whether they were driven by common genetic factors using pairwise genetic correlations. Subsequently, we derived activation maps associated with cognitive tasks via functional imaging meta-analysis in BrainMap (N ¼ 4484), and tested whether cognitive traits that shared genetic variation also exhibited overlapping brain activation. Our genetic analysis determined that six cognitive measures (cognitive flexibility, no-go continuous performance, fluid intelligence, processing speed, reading decoding and vocabulary comprehension) were heritable (0.3 < h2 < 0.5), and genetically correlated with at least one other heritable cognitive measure (0.2 < ρg < 0.35). The meta-analysis showed that two genetically-correlated traits, cognitive flexibility and fluid intelligence (ρg ¼ 0.24), also had a significant brain activation overlap (ρperm ¼ 0.29). These findings indicate that fluid intelligence and cognitive flexibility rely on overlapping biological features, both at the neural systems level and at the molecular level. The cross-disciplinary approach we introduce provides a concrete framework for data-driven quantification of biological convergence between genetics, brain function, and behavior in health and disease.
Keywords: Shared genetics | Functional imaging meta-analysis | Brain activation overlap | Cognition | Biological convergence
Harmonization of large MRI datasets for the analysis of brain imaging patterns throughout the lifespan
هماهنگ سازی مجموعه داده های بزرگ MRI برای تجزیه و تحلیل الگوهای تصویربرداری از مغز در طول عمر-2020
As medical imaging enters its information era and presents rapidly increasing needs for big data analytics, robust pooling and harmonization of imaging data across diverse cohorts with varying acquisition protocols have become critical. We describe a comprehensive effort that merges and harmonizes a large-scale dataset of 10,477 structural brain MRI scans from participants without a known neurological or psychiatric disorder from 18 different studies that represent geographic diversity. We use this dataset and multi-atlas-based image processing methods to obtain a hierarchical partition of the brain from larger anatomical regions to individual cortical and deep structures and derive age trends of brain structure through the lifespan (3–96 years old). Critically, we present and validate a methodology for harmonizing this pooled dataset in the presence of nonlinear age trends. We provide a web-based visualization interface to generate and present the resulting age trends, enabling future studies of brain structure to compare their data with this reference of brain development and aging, and to examine deviations from ranges, potentially related to disease.
Keywords: MRI | Segmentation | FreeSurfer | MUSE | Brain | ROI
Imaging of microdefects in ZnGeP2 single crystals by X-ray topography
تصویربرداری از ریزگردها در بلورهای تک ZnGeP2 توسط توپوگرافی با اشعه X-2020
The contrast from microdefects in ZnGeP2 crystals is studied. Simulation of images in X-ray topography based on the Borrmann effect is carried out for a model of a coherent inclusion of spherical form in an infinite isotropic matrix. For this simulation, a semiphenomenological theory of contrast from defects with a slowly changing deformation field is applied. It is shown that the contrast from the inclusion is a complex function, depending on the nature of defect (sign of the deformation of the matrix), the magnitude of the deformation caused by the defect, its depth in the crystal, the modulus of the diffraction vector g and the topography used (reflection or transmission). The most common images are intensity rosettes of double or triple contrast, whose lobes are elongated along the diffraction vector. These are created by inclusions, located near the X-ray exit surface of the sample. Analysis of experimental data shows that the majority of microdefects in ZnGeP2 revealed by Borrmann method (~96%) show good agreement with proposed model. All the features of the experimental images are explained by the theory. Additionally, the contrast from dislocation loops and from groups of big inclusions which have non-Coulombic deformation fields is observed
Keywords: B2. Nonlinear optic materials | A2. Bridgman technique | A2. Seed crystals | A1. Xray topography | A1. Defects| A1. Computer simulation
تحلیل لبه ای مبتنی بر موجک چند جهته برای تشخیص سطح توسط پروفیلومتری نوری
سال انتشار: 2019 - تعداد صفحات فایل pdf انگلیسی: 10 - تعداد صفحات فایل doc فارسی: 18
دانشمندان، مهندسان و تولید کنندگان نیاز ضروری به تکنیک های بهتر تشخیص و کنترل کیفیت دارند. مترولوژی نوری با استفاده از علوم نور و علوم کامپیوتر به دنبال شبیه سازی، طراحی، محاسبات و بازرسی برای بسیاری از برنامه های کاربردی علمی و صنعتی مانند اپتیک، مکانیک، هواپیما، الکترونیک و … است. آنالیز الگوی fringe روشی برای انجام برخی عملیات در تصاویر نوری و به منظور دریافت نقشه فاز اینترفرومتری و سپس استخراج برخی اطلاعات مفید از آن است. در این مقاله، بهبود محرک الگوریتم دمدولاسیون fringe محلی ارائه شده است، که بر اساس موجک جدید چند جهته است. کارهای عددی و تجربی در مقایسه با سایر الگوریتم های استاندارد، سود جالبی را نشان می دهد. رویکرد ما به سرعت به عنوان فاز روش های بازیابی پرطرفدار اجرا می شود، اما با دقت قابل توجهی دمدولاسیون fringe های نویز را بهبود می دهد. همه این مسائل بدون هیچ پیش پردازش توسط فیلتر کردن مدل ها رخ می دهد.
کليدواژه ها: تصویربرداری نوری | علوم کامپیوتر | پردازش تصویر | موجک چند جهته | فاز بازیابی | طرح ریزی fringe .
|مقاله ترجمه شده|
TOP-GAN: Stain-free cancer cell classification using deep learning with a small training set
TOP-GAN: طبقه بندی سلول های سرطانی بدون لکه با استفاده از یادگیری عمیق با یک مجموعه آموزشی کوچک-2019
We propose a new deep learning approach for medical imaging that copes with the problem of a small training set, the main bottleneck of deep learning, and apply it for classification of healthy and cancer cell lines acquired by quantitative phase imaging. The proposed method, called transferring of pre-trained generative adversarial network (TOP-GAN), is hybridization between transfer learning and generative ad- versarial networks (GANs). Healthy cells and cancer cells of different metastatic potential have been im- aged by low-coherence off-axis holography. After the acquisition, the optical path delay maps of the cells are extracted and directly used as inputs to the networks. In order to cope with the small number of clas- sified images, we use GANs to train a large number of unclassified images from another cell type (sperm cells). After this preliminary training, we change the last layers of the network and design automatic classifiers for the correct cell type (healthy/primary cancer/metastatic cancer) with 90–99% accuracies, although small training sets of down to several images are used. These results are better in comparison to other classic methods that aim at coping with the same problem of a small training set. We believe that our approach makes the combination of holographic microscopy and deep learning networks more accessible to the medical field by enabling a rapid, automatic and accurate classification in stain-free imaging flow cytometry. Furthermore, our approach is expected to be applicable to many other medical image classification tasks, suffering from a small training set.
Keywords: Holography | Quantitative phase imaging | Deep learning | Machine learning algorithms | Image classification | Biological cells
Neurobiological divergence of the positive and negative schizophrenia subtypes identified upon a new factor-structure of psychopathology using non-negative factorization: An international machine-learning study
واگرایی عصبی از زیرگروه های اسکیزوفرنی مثبت و منفی مشخص شده بر یک ساختار جدید از روانشناسی با استفاده از فاکتورسازی غیر منفی: یک مطالعه بین المللی یادگیری ماشین-2019
Objective: Disentangling psychopathological heterogeneity in schizophrenia is challenging and previous results remain inconclusive. We employed advanced machine-learning to identify a stable and generalizable factorization of the “Positive and Negative Syndrome Scale (PANSS)”, and used it to identify psychopathological subtypes as well as their neurobiological differentiations. Methods: PANSS data from the Pharmacotherapy Monitoring and Outcome Survey cohort (1545 patients, 586 followed up after 1.35±0.70 years) were used for learning the factor-structure by an orthonormal projective non-negative factorization. An international sample, pooled from nine medical centers across Europe, USA, and Asia (490 patients), was used for validation. Patients were clustered into psychopathological subtypes based on the identified factor-structure, and the neurobiological divergence between the subtypes was assessed by classification analysis on functional MRI connectivity patterns. Results: A four-factor structure representing negative, positive, affective, and cognitive symptoms was identified as the most stable and generalizable representation of psychopathology. It showed higher internal consistency than the original PANSS subscales and previously proposed factor-models. Based on this representation, the positive-negative dichotomy was confirmed as the (only) robust psychopathological subtypes, and these subtypes were longitudinally stable in about 80% of the repeatedly assessed patients. Finally, the individual subtype could be predicted with good accuracy from functional connectivity profiles of the ventro-medial frontal cortex, temporoparietal junction, and precuneus. Conclusions: Machine-learning applied to multi-site data with cross-validation yielded a factorization generalizable across populations and medical systems. Together with subtyping and the demonstrated ability to predict subtype membership from neuroimaging data, this work further disentangles the heterogeneity in schizophrenia
Keywords: non-negative factorization | brain imaging | subtyping | machine learning | multivariate classification | schizophrenia
Combined machine learning and diffusion tensor imaging reveals altered anatomic fiber connectivity of the brain in primary open-angle glaucoma
یادگیری ماشین ترکیبی و تصویربرداری با تانسور انتشار ، ارتباط فیبر آناتومیک مغز را در گلوکوم زاویه باز اولیه تغییر داده است-2019
Parameters derived from diffusion tensor imaging (DTI) have been found to be significantly altered in the optic tracts, optic nerves, and optic radiations in patients with primary open-angle glaucoma (POAG). In this study, DTI-derived parameters were further constructed into fiber connectivity, and we investigated anatomical fiber connectivity changes within and beyond the visual pathway in POAG patients. DTI and T1-weighted magnetic resonance images were acquired in 18 POAG patients and 26 healthy controls (HC). White matter tracts based on the Brodmann atlases (BA) were constructed using the deterministic fiber tracking method. The mean fractional anisotropy (FA), fiber number (FN), and mean fiber length (FL) were measured and then evaluated using twosample t-tests between POAG and HC. The fiber connectivity between regions was taken as the features for classifying HC and POAG using a machine learning method known as naïve Bayesian classification. The mean FA decreased in connections between visual cortex BA17/BA18 and cortex BA23/BA25/BA35/BA36, while it increased in the connections between cortex BA3/BA7/BA9 and BA5/BA6/BA45/BA25 in POAG. Classification using fibers where a significant difference in FN had been identified produced better accuracy (ACC=0.89) than using FA or FL (ACC=0.77 and 0.75, respectively). The FN of individual fiber connections with higher accuracy and significant changes in POAG involved brain regions associated with vision (BA19), depression (BA10/BA46/ BA25), and memory (BA29). These findings strengthen the hypothesis that POAG involves changes in anatomical connectivity within and beyond the visual pathway. Classification using the machine learning method reveals that mean FN has the potential to be used as a biomarker for detecting white matter microstructure changes in POAG.
Keywords: Glaucoma | Anatomic white matter connectivity | Diffusion tensor imaging | Fiber tracking | Machine learning