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quantitative image analysis

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https://www.readbyqxmd.com/read/28934631/picometer-scale-atom-position-analysis-in-annular-bright-field-stem-imaging
#1
Peng Gao, Akihito Kumamoto, Ryo Ishikawa, Nathan Lugg, Naoya Shibata, Yuichi Ikuhara
We study the effects of specimen mistilt on the picometer-scale measurement of local structure by combing experiment and simulation in annular bright-field scanning transmission electron microscopy (ABF-STEM). A relative distance measurement method is proposed to separate the tilt effects from the scan noise and sample drift induced image distortion. We find that under a typical experimental condition a small specimen tilt (∼6 mrad) in 25 nm thick SrTiO3 along [001] causes 11.9 pm artificial displacement between O and Sr/TiO columns in ABF image, which is more than 3 times of scan noise and sample drift induced image distortion ∼3...
September 11, 2017: Ultramicroscopy
https://www.readbyqxmd.com/read/28934247/the-extent-of-intrauterine-growth-restriction-determines-the-severity-of-cerebral-injury-and-neurobehavioural-deficits-in-rodents
#2
Crystal A Ruff, Stuart D Faulkner, Prakasham Rumajogee, Stephanie Beldick, Warren Foltz, Jennifer Corrigan, Alfred Basilious, Shangjun Jiang, Shanojan Thiyagalingam, Jerome Y Yager, Michael G Fehlings
BACKGROUND: Cerebral Palsy (CP) is the most common physical pediatric neurodevelopmental disorder and spastic diplegic injury is its most frequent subtype. CP results in substantial neuromotor and cognitive impairments that have significant socioeconomic impact. Despite this, its underlying pathophysiological mechanisms and etiology remain incompletely understood. Furthermore, there is a need for clinically relevant injury models, which a) reflect the heterogeneity of the condition and b) can be used to evaluate new translational therapies...
2017: PloS One
https://www.readbyqxmd.com/read/28934236/automated-computer-assisted-quantitative-analysis-of-intact-murine-lungs-at-the-alveolar-scale
#3
Goran Lovric, Ioannis Vogiatzis Oikonomidis, Rajmund Mokso, Marco Stampanoni, Matthias Roth-Kleiner, Johannes C Schittny
Using state-of-the-art X-ray tomographic microscopy we can image lung tissue in three dimensions in intact animals down to a micrometer precision. The structural complexity and hierarchical branching scheme of the lung at this level of details, however, renders the extraction of biologically relevant quantities particularly challenging. We have developed a methodology for a detailed description of lung inflation patterns by measuring the size and the local curvature of the parenchymal airspaces. These quantitative tools for morphological and topological analyses were applied to high-resolution murine 3D lung image data, inflated at different pressure levels under immediate post mortem conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28933333/-canine-elbow-humeroulnar-incongruity-measurements-using-computed-tomography
#4
R Snášil, P Proks, A Nečasová, K Michalčáková, A Nečas
PURPOSE OF THE STUDY The purpose of the study is to compare the repeatability and reproducibility of quantitative and subjective evaluation of elbow humeroulnar incongruity (HUI) using computed tomography (CT) on an in vivo canine model. MATERIAL AND METHODS HUI was evaluated on canine (n = 50) elbow joints (n = 100). The computed tomography of elbow joints was performed under intravenous sedation. Multiplanar reconstructions (MPR) were produced. HUI was evaluated on sagittal MPR images subjectively and by measuring the subluxation index (SI)...
2017: Acta Chirurgiae Orthopaedicae et Traumatologiae Cechoslovaca
https://www.readbyqxmd.com/read/28932698/quantitative-magnetic-resonance-mr-neurography-for-evaluation-of-peripheral-nerves-and-plexus-injuries
#5
REVIEW
Teodoro Martín Noguerol, Rafael Barousse, Mariano Socolovsky, Antonio Luna
Traumatic conditions of peripheral nerves and plexus have been classically evaluated by morphological imaging techniques and electrophysiological tests. New magnetic resonance imaging (MRI) studies based on 3D fat-suppressed techniques are providing high accuracy for peripheral nerve injury evaluation from a qualitative point of view. However, these techniques do not provide quantitative information. Diffusion weighted imaging (DWI) and diffusion tensor imaging (DTI) are functional MRI techniques that are able to evaluate and quantify the movement of water molecules within different biological structures...
August 2017: Quantitative Imaging in Medicine and Surgery
https://www.readbyqxmd.com/read/28932696/an-automated-workflow-for-quantifying-rna-transcripts-in-individual-cells-in-large-data-sets
#6
Matthew C Pharris, Tzu-Ching Wu, Xinping Chen, Xu Wang, David M Umulis, Vikki M Weake, Tamara L Kinzer-Ursem
Advanced molecular probing techniques such as single molecule fluorescence in situ hybridization (smFISH) or RNAscope can be used to assess the quantity and spatial location of mRNA transcripts within cells. Quantifying mRNA expression in large image sets usually involves automated counting of fluorescent spots. Though conventional spot counting algorithms may suffice, they often lack high-throughput capacity and accuracy in cases of crowded signal or excessive noise. Automatic identification of cells and processing of many images is still a challenge...
2017: MethodsX
https://www.readbyqxmd.com/read/28932538/the-value-of-delayed-phase-enhanced-imaging-in-malignant-pleural-mesothelioma
#7
Akash M Patel, Ian Berger, E Paul Wileyto, Urooj Khalid, Drew A Torigian, Arun C Nachiappan, Eduardo M Barbosa, Warren B Gefter, Maya Galperin-Aizenberg, Narainder K Gupta, Charles B Simone, Andrew R Haas, Evan W Alley, Sunil Singhal, Keith A Cengel, Sharyn I Katz
BACKGROUND: Cross-sectional imaging of malignant pleural mesothelioma (MPM) can underestimate the presence of local tumor invasion. Since accurate staging is vital optimal choice of therapy, techniques that optimize pleural imaging are needed. Here we estimate the optimal timing of MPM enhancement on magnetic resonance imaging (MRI). METHODS: All MPM patients with intravenous (IV) contrast enhanced staging MRI between 2000-2016 at our institution were retrospectively selected for image analysis...
August 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28932207/model-based-magnetization-transfer-imaging-markers-to-characterize-patients-and-asymptomatic-gene-carriers-in-huntington-s-disease
#8
Roland Wiest, Jean-Marc Burgunder, Claus Kiefer
BACKGROUND AND PURPOSE: Huntington's disease (HD) is a chronic progressive neurodegenerative disorder with a long presymptomatic period that opens a window for potential therapies aimed at neuroprotection. Neuroimaging offers the potential to monitor disease-related progression of the disease burden (DB) using model-based magnetization transfer imaging. MATERIALS AND METHODS: We have conducted a cross-sectional study to stratify healthy age-matched controls, premanifest and symptomatic HD patients (n = 30) according to their macromolecular depositions in the caudate nucleus...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28932029/validation-of-immunoexpression-of-tenascin-c-in-oral-precancerous-and-cancerous-tissues-using-imagej-analysis-with-novel-immunohistochemistry-profiler-plugin-an-immunohistochemical-quantitative-analysis
#9
Deepa Rajesh Mane, Alka D Kale, Chetan Belaldavar
BACKGROUND: Immunohistochemistry (IHC) is a molecular technique that has grown tremendously over the years. However, the assessment is only qualitative which is subjective and causes errors. Due to this limitation, several excellent markers have not gained importance and reached clinical trials. Hence, we aimed to quantify IHC by ImageJ analysis with a novel IHC profiler plugin. ImageJ has not been tried in oral precancerous tissues with minimal attempt for matrix markers. AIM: This study aimed to validate the quantification of immunoexpression of tenascin-C (TN-C) in oral precancerous tissues and oral squamous cell carcinoma (OSCC) using ImageJ software with IHC profiler plugin...
May 2017: Journal of Oral and Maxillofacial Pathology: JOMFP
https://www.readbyqxmd.com/read/28931626/pacequant-a-tool-for-high-throughput-quantification-of-pavement-cell-shape-characteristics
#10
Birgit Möller, Yvonne Poeschl, Romina Plötner, Katharina Bürstenbinder
Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw puzzle shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity...
September 20, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28931601/local-cellular-neighbourhood-controls-proliferation-in-cell-competition
#11
Anna Bove, Daniel Gradeci, Yasuyuki Fujita, Shiladitya Banerjee, Guillaume Charras, Alan R Lowe
Cell competition is a quality control mechanism through which tissues eliminate unfit cells. Cell competition can result from short-range biochemical inductions or long-range mechanical cues. However, little is known about how cell-scale interactions give rise to population shifts in tissues, due to the lack of experimental and computational tools to efficiently characterise interactions at the single-cell level. Here, we address these challenges by combining long-term automated microscopy with deep learning image analysis to decipher how single-cell behaviour determines tissue make-up during competition...
September 20, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28931522/three-dimensional-morphometric-analysis-of-the-renal-vasculature
#12
Zohaib Khan, Jennifer P Ngo, Bianca Le, Roger G Evans, James Todd Pearson, Bruce S Gardiner, David W Smith
Vascular topology and morphology is critical in the regulation of blood flow and the transport of small solutes including oxygen, carbon dioxide, nitric oxide and hydrogen sulfide. Renal vascular morphology is particularly challenging as many arterial walls are partially wrapped by the walls of veins. In the absence of a precise characterization of three-dimensional branching vascular geometry, accurate computational modeling of the intrarenal transport of small diffusible molecules is impossible. An enormous manual effort was required to achieve a relatively precise characterization of rat renal vascular geometry, highlighting the need for an automated method for analysis of branched vasculature morphology to allow characterization of the renal vascular geometry of other species, including humans...
September 20, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/28931389/semi-automated-quantification-of-hard-exudates-in-colour-fundus-photographs-diagnosed-with-diabetic-retinopathy
#13
Abhilash Goud Marupally, Kiran Kumar Vupparaboina, Hari Kumar Peguda, Ashutosh Richhariya, Soumya Jana, Jay Chhablani
BACKGROUND: Hard exudates (HEs) are the classical sign of diabetic retinopathy (DR) which is one of the leading causes of blindness, especially in developing countries. Accordingly, disease screening involves examining HEs qualitatively using fundus camera. However, for monitoring the treatment response, quantification of HEs becomes crucial and hence clinicians now seek to measure the area of HEs in the digital colour fundus (CF) photographs. Against this backdrop, we proposed an algorithm to quantify HEs using CF images and compare with previously reported technique using ImageJ...
September 20, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/28931067/in-vivo-imaging-system-for-explants-analysis-a-new-approach-for-assessment-of-cell-transplantation-effects-in-large-animal-models
#14
Weronika Zarychta-Wiśniewska, Anna Burdzinska, Radosław Zagozdzon, Bartosz Dybowski, Marta Butrym, Zdzisław Gajewski, Leszek Paczek
INTRODUCTION: Despite spectacular progress in cellular transplantology, there are still many concerns about the fate of transplanted cells. More preclinical studies are needed, especially on large animal models, to bridge the translational gap between basic research and the clinic. Herein, we propose a novel approach in analysis of cell transplantation effects in large animals explants using in vivo imaging system (IVIS®) or similar equipment. MATERIAL AND METHODS: In the in vitro experiment cells labeled with fluorescent membrane dyes: DID (far red) or PKH26 (orange) were visualized with IVIS®...
2017: PloS One
https://www.readbyqxmd.com/read/28930805/the-value-of-diffusion-weighted-imaging-in-combination-with-conventional-magnetic-resonance-imaging-for-improving-tumor-detection-for-early-cervical-carcinoma-treated-with-fertility-sparing-surgery
#15
Xiulei Li, Ling Wang, Yong Li, Peiji Song
OBJECTIVE: This study aimed to investigate the value of diffusion-weighted imaging (DWI) in combination with conventional magnetic resonance imaging (MRI) for improving tumor detection in young patients treated with fertility-sparing surgery because of early cervical carcinoma. METHODS: Fifty-four patients with stage Ia or Ib1 cervical carcinoma were enrolled into this study. Magnetic resonance examinations were performed for these patients using conventional MRI (including T1-weighted imaging, T2-weighted imaging, and dynamic contrast-enhanced MRI) and DWI...
September 19, 2017: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/28930613/an-automated-approach-for-early-detection-of-diabetic-retinopathy-using-sd-oct-images
#16
Ahmed H ElTanboly, Agustina Palacio, Ahmed M Shalaby, Andrew E Switala, Omar Helmy, Shlomit Schaal, Ayman El-Baz
  This study was to demonstrate the feasibility of an automatic approach for early detection of diabetic retinopathy (DR) from SD-OCT images. These scans were prospectively collected from 200 subjects through the fovea then were automatically segmented, into 12 layers. Each layer was characterized by its thickness, tortuosity, and normalized reflectivity. 26 diabetic patients, without DR changes visible by funduscopic examination, were matched with 26 controls, according to age and sex, for purposes of statistical analysis using mixed effects ANOVA...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
https://www.readbyqxmd.com/read/28930453/ab-initio-qm-mm-modelling-of-the-rate-limiting-proton-transfer-step-in-the-deamination-of-tryptamine-by-aromatic-amine-dehydrogenase
#17
Kara Elizabeth Ranaghan, William G Morris, Laura Masgrau, Kittusamy Senthilkumar, Linus O Johannissen, Nigel S Scrutton, Jeremy N Harvey, Frederick R Manby, Adrian J Mulholland
Aromatic amine dehydrogenase (AADH) and related enzymes are at the heart of debates on the roles of quantum tunnelling and protein dynamics in catalysis. The reaction of tryptamine in AADH involves significant quantum tunnelling in the rate-limiting proton transfer step, shown e.g. by large H/D primary kinetic isotope effects (KIEs), with unusual temperature dependence. We apply correlated ab initio combined quantum mechanics/molecular mechanics (QM/MM) methods, at levels up to local coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), to calculate accurate potential energy surfaces for this reaction, which are necessary for quantitative analysis of tunnelling contributions and reaction dynamics...
September 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28929243/discrimination-between-benign-and-malignant-breast-lesions-using-volumetric-quantitative-dynamic-contrast-enhanced-mr-imaging
#18
Ziliang Cheng, Zhuo Wu, Guangzi Shi, Zhilong Yi, Mingwei Xie, Weike Zeng, Chao Song, Chushan Zheng, Jun Shen
OBJECTIVE: To determine the diagnostic performance of volumetric quantitative dynamic contrast-enhanced MRI (qDCE-MRI) in differentiation between malignant and benign breast lesions. METHODS: DCE-MRI was performed in 124 patients with 136 breast lesions. Quantitative pharmacokinetic parameters K(trans), Kep, Ve, Vp and semi-quantitative parameters TTP, MaxCon, MaxSlope, AUC were obtained by using a two-compartment extended Tofts model and three-dimensional volume of interest...
September 19, 2017: European Radiology
https://www.readbyqxmd.com/read/28929112/imaging-diagnosis-of-right-ventricle-involvement-in-chagas-cardiomyopathy
#19
REVIEW
Minna M D Romano, Henrique T Moreira, André Schmidt, Benedito Carlos Maciel, José Antônio Marin-Neto
Right ventricle (RV) is considered a neglected chamber in cardiology and knowledge about its role in cardiac function was mostly focused on ventricular interdependence. However, progress on the understanding of myocardium diseases primarily involving the RV led to a better comprehension of its role in health and disease. In Chagas disease (CD), there is direct evidence from both basic and clinical research of profound structural RV abnormalities. However, clinical detection of these abnormalities is hindered by technical limitations of imaging diagnostic tools...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28928814/nuclear-features-of-infiltrating-urothelial-carcinoma-are-distinguished-from-low-grade-noninvasive-papillary-urothelial-carcinoma-by-image-analysis
#20
Noritake Kosuge, Masanao Saio, Hirofumi Matsumoto, Hajime Aoyama, Akiko Matsuzaki, Naoki Yoshimi
Recent advances in computer technology have been made and image analysis (IA) has been introduced into pathological fields. The present study aimed to investigate the utility of IA for the evaluation of nuclear features and staining of immunohistochemistry (IHC) for Ki-67, p53 and GATA-binding protein 3 (GATA-3) in urothelial carcinoma tissue samples. A total of 49 cases of urothelial carcinoma tissue samples were obtained by transurethral resection of bladder tumors, which included 11 low-grade papillary urothelial carcinomas (LGPUCs), 1 non-invasive high-grade urothelial carcinoma and 37 infiltrating urothelial carcinomas (IUCs)...
September 2017: Oncology Letters
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