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quantitative image analysis

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https://www.readbyqxmd.com/read/28806574/quantitative-diffusion-weighted-magnetic-resonance-imaging-assessment-of-chemotherapy-treatment-response-of-pediatric-osteosarcoma-and-ewing-sarcoma-malignant-bone-tumors
#1
Andrew J Degnan, Chul Y Chung, Amisha J Shah
OBJECTIVE: Assessment of tumor response to chemotherapy is essential in managing malignant pediatric bone tumors prior to resection. SUBJECTS AND METHODS: Pre-chemotherapy and post-chemotherapy osteosarcoma and Ewing sarcoma cases (n=18) were analyzed with apparent diffusion coefficient (ADC) values measured by two readers. RESULTS: Treated tumors demonstrated significantly greater ADC values compared to untreated tumors (p<0.001). Intraclass correlation coefficients ranged between 0...
August 5, 2017: Clinical Imaging
https://www.readbyqxmd.com/read/28806525/imaging-the-localized-plasmon-resonance-modes-in-graphene-nanoribbons
#2
Fengrui Hu, Yilong Luan, Zhe Fei, Igor Palubski, Michael Goldflam, Siyuan Dai, Jhih-Sheng Wu, Kirk W Post, Guido Janssen, Michael M Fogler, D N Basov
We report a nano-infrared (IR) imaging study of the localized plasmon resonance modes of graphene nanoribbons (GNRs) using a scattering-type scanning near-field optical microscope (s-SNOM). By comparing the imaging data of GNRs that are aligned parallel and perpendicular to the in-plane component of the excitation laser field, we observed symmetric and asymmetric plasmonic interference fringes, respectively. Theoretical analysis indicates that the asymmetric fringes are formed due to the interplay between the localized surface plasmon resonance (SPR) mode excited by the GNRs and the propagative surface plasmon polariton (SPP) mode launched by the s-SNOM tip...
August 14, 2017: Nano Letters
https://www.readbyqxmd.com/read/28805805/whole-tumor-section-quantitative-image-analysis-maximizes-between-pathologists-reproducibility-for-clinical-immunohistochemistry-based-biomarkers
#3
Michael Barnes, Chukka Srinivas, Isaac Bai, Judith Frederick, Wendy Liu, Anindya Sarkar, Xiuzhong Wang, Yao Nie, Bryce Portier, Monesh Kapadia, Olcay Sertel, Elizabeth Little, Bikash Sabata, Jim Ranger-Moore
Pathologists have had increasing responsibility for quantitating immunohistochemistry (IHC) biomarkers with the expectation of high between-reader reproducibility due to clinical decision-making especially for patient therapy. Digital imaging-based quantitation of IHC clinical slides offers a potential aid for improvement; however, its clinical adoption is limited potentially due to a conventional field-of-view annotation approach. In this study, we implemented a novel solely morphology-based whole tumor section annotation strategy to maximize image analysis quantitation results between readers...
August 14, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28804731/eye-tracking-in-catheter-based-cardiovascular-interventions-early-results
#4
Peter Lanzer, Mohammad Al-Naser, Syed Saqib Bukhari, Andreas Dengel, Elizabeth A Krupinski
Visual x-ray image processing (XRIP) represents a fundamental component of catheter-based cardiovascular interventions (CBCVIs). To date, no data are available to define XRIP in this setting. To characterize CBCVI XRIP, we developed a computer-based method allowing continuous temporal-spatial analysis of data recorded by a head-mounted eye-tracking device. Quantitative analysis of gaze duration of an expert operator (EO) revealed that the average time in minutes spent viewing the images on the display screen was [Formula: see text] and [Formula: see text] of the total recorded time in coronary angiography (CA) and in CA followed by CBCVI, respectively...
July 2017: Journal of Medical Imaging
https://www.readbyqxmd.com/read/28804569/dynamic-registration-for-gigapixel-serial-whole-slide-images
#5
Blair J Rossetti, Fusheng Wang, Pengyue Zhang, George Teodoro, Daniel J Brat, Jun Kong
High-throughput serial histology imaging provides a new avenue for the routine study of micro-anatomical structures in a 3D space. However, the emergence of serial whole slide imaging poses a new registration challenge, as the gigapixel image size precludes the direct application of conventional registration techniques. In this paper, we develop a three-stage registration with multi-resolution mapping and propagation method to dynamically produce registered subvolumes from serial whole slide images. We validate our algorithm with gigapixel images of serial brain tumor sections and synthetic image volumes...
April 2017: Proceedings of the IEEE International Symposium on Biomedical Imaging: from Nano to Macro
https://www.readbyqxmd.com/read/28802623/an-analytical-model-which-determines-the-apparent-t1-for-modified-look-locker-inversion-recovery-analysis-of-the-longitudinal-relaxation-under-the-influence-of-discontinuous-balanced-classical-molli-and-spoiled-gradient-echo-readouts
#6
Thomas Kampf, Theresa Reiter, Wolfgang Rudolf Bauer
Quantitative nuclear magnetic resonance imaging (MRI) shifts more and more into the focus of clinical research. Especially determination of relaxation times without/and with contrast agents becomes the foundation of tissue characterization, e.g. in cardiac MRI for myocardial fibrosis. Techniques which assess longitudinal relaxation times rely on repetitive application of readout modules, which are interrupted by free relaxation periods, e.g. the Modified Look-Locker Inversion Recovery = MOLLI sequence. These discontinuous sequences reveal an apparent relaxation time, and, by techniques extrapolated from continuous readout sequences, a putative real T1 is determined...
August 9, 2017: Zeitschrift Für Medizinische Physik
https://www.readbyqxmd.com/read/28802145/ensemble-of-expert-deep-neural-networks-for-spatio-temporal-denoising-of-contrast-enhanced-mri-sequences
#7
A Benou, R Veksler, A Friedman, T Riklin Raviv
Dynamic contrast-enhanced MRI (DCE-MRI) is an imaging protocol where MRI scans are acquired repetitively throughout the injection of a contrast agent. The analysis of dynamic scans is widely used for the detection and quantification of blood-brain barrier (BBB) permeability. Extraction of the pharmacokinetic (PK) parameters from the DCE-MRI concentration curves allows quantitative assessment of the integrity of the BBB functionality. However, curve fitting required for the analysis of DCE-MRI data is error-prone as the dynamic scans are subject to non-white, spatially-dependent and anisotropic noise...
August 2, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28801901/functional-screening-of-core-promoter-activity
#8
Dan Y Even, Adi Kedmi, Diana Ideses, Tamar Juven-Gershon
The core promoter is the DNA sequence that recruits the basal transcription machinery and directs accurate initiation of transcription. It is an active contributor to gene expression that can be rationally designed to manipulate the levels of expression. Core promoter function can be analyzed using different experimental approaches. Here, we describe the qualitative and quantitative analysis of engineered core promoter functions using the EGFP reporter gene that is driven by distinct core promoters. Expression plasmids are transfected into different mammalian cell lines, and the resulting fluorescence is monitored by live cell imaging , as well as by flow cytometry...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28801836/optimization-of-sample-preparation-and-instrumental-parameters-for-the-rapid-analysis-of-drugs-of-abuse-in-hair-samples-by-maldi-ms-ms-imaging
#9
Bryn Flinders, Emma Beasley, Ricky M Verlaan, Eva Cuypers, Simona Francese, Tom Bassindale, Malcolm R Clench, Ron M A Heeren
Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) has been employed to rapidly screen longitudinally sectioned drug user hair samples for cocaine and its metabolites using continuous raster imaging. Optimization of the spatial resolution and raster speed were performed on intact cocaine contaminated hair samples. The optimized settings (100 × 150 μm at 0.24 mm/s) were subsequently used to examine longitudinally sectioned drug user hair samples. The MALDI-MS/MS images showed the distribution of the most abundant cocaine product ion at m/z 182...
August 11, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28801817/contour-segmentation-of-the-intima-media-and-adventitia-layers-in-intracoronary-oct-images-application-to-fully-automatic-detection-of-healthy-wall-regions
#10
Guillaume Zahnd, Ayla Hoogendoorn, Nicolas Combaret, Antonios Karanasos, Emilie Péry, Laurent Sarry, Pascal Motreff, Wiro Niessen, Evelyn Regar, Gijs van Soest, Frank Gijsen, Theo van Walsum
PURPOSE: Quantitative and automatic analysis of intracoronary optical coherence tomography images is useful and time-saving to assess cardiovascular risk in the clinical arena. METHODS: First, the interfaces of the intima, media, and adventitia layers are segmented, by means of an original front propagation scheme, running in a 4D multi-parametric space, to simultaneously extract three non-crossing contours in the initial cross-sectional image. Second, information resulting from the tentative contours is exploited by a machine learning approach to identify healthy and diseased regions of the arterial wall...
August 11, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28801575/limits-of-radiomic-based-entropy-as-a-surrogate-of-tumor-heterogeneity-roi-area-acquisition-protocol-and-tissue-site-exert-substantial-influence
#11
Laurent Dercle, Samy Ammari, Mathilde Bateson, Paul Blanc Durand, Eva Haspinger, Christophe Massard, Cyril Jaudet, Andrea Varga, Eric Deutsch, Jean-Charles Soria, Charles Ferté
Entropy is a promising quantitative imaging biomarker for characterizing cancer imaging phenotype. Entropy has been associated with tumor gene expression, tumor metabolism, tumor stage, patient prognosis, and treatment response. Our hypothesis states that tumor-specific biomarkers such as entropy should be correlated between synchronous metastases. Therefore, a significant proportion of the variance of entropy should be attributed to the malignant process. We analyzed 112 patients with matched/paired synchronous metastases (SM#1 and SM#2) prospectively enrolled in the MOSCATO-01 clinical trial...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801168/please-don-t-move-evaluating-motion-artifact-from-peripheral-quantitative-computed-tomography-scans-using-textural-features
#12
Timo Rantalainen, Paola Chivers, Belinda R Beck, Sam Robertson, Nicolas H Hart, Sophia Nimphius, Benjamin K Weeks, Fleur McIntyre, Beth Hands, Aris Siafarikas
Most imaging methods, including peripheral quantitative computed tomography (pQCT), are susceptible to motion artifacts particularly in fidgety pediatric populations. Methods currently used to address motion artifact include manual screening (visual inspection) and objective assessments of the scans. However, previously reported objective methods either cannot be applied on the reconstructed image or have not been tested for distal bone sites. Therefore, the purpose of the present study was to develop and validate motion artifact classifiers to quantify motion artifact in pQCT scans...
August 8, 2017: Journal of Clinical Densitometry
https://www.readbyqxmd.com/read/28800674/the-genetic-encoded-toolbox-for-electron-microscopy-and-connectomics
#13
REVIEW
Ryuichi Shigemoto, Maximilian Joesch
Developments in bioengineering and molecular biology have introduced a palette of genetically encoded probes for identification of specific cell populations in electron microscopy. These probes can be targeted to distinct cellular compartments, rendering them electron dense through a subsequent chemical reaction. These electron densities strongly increase the local contrast in samples prepared for electron microscopy, allowing three major advances in ultrastructural mapping of circuits: genetic identification of circuit components, targeted imaging of regions of interest and automated analysis of the tagged circuits...
August 11, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28800625/variability-in-quantitative-analysis-of-atherosclerotic-plaque-inflammation-using-18f-fdg-pet-ct
#14
Karel-Jan D F Lensen, Alper M van Sijl, Alexandre E Voskuyl, Conny J van der Laken, Martijn W Heymans, Emile F I Comans, Mike T Nurmohamed, Yvo M Smulders, Ronald Boellaard
BACKGROUND: 18F-FDG-PET(/CT) is increasingly used in studies aiming at quantifying atherosclerotic plaque inflammation. Considerable methodological variability exists. The effect of data acquisition and image analysis parameters on quantitative uptake measures, such as standardized uptake value (SUV) and target-to-background ratio (TBR) has not been investigated extensively. OBJECTIVE: The goal of this study was to explore the effect of several data acquisition and image analysis parameters on quantification of vascular wall 18F-FDG uptake measures, in order to increase awareness of potential variability...
2017: PloS One
https://www.readbyqxmd.com/read/28799616/quantitative-investigation-of-mda-mb-231-breast-cancer-cell-motility-dependence-on-epidermal-growth-factor-concentration-and-its-gradient
#15
Tanzila Islam, Haluk Resat
Enhanced cell motility is one of the primary features of cancer. Accumulated evidence demonstrates that Epidermal Growth Factor Receptor (EGFR) mediated pathways play an important role in breast cancer cell proliferation and migration. We have quantified the MDA-MB-231 breast cancer cell migration in response to the stimulation of EGFR pathways with their ligand EGF to determine how the cell motility of MDA-MB-231 cells depends on the ligand concentration and gradient. Analysis at the single cell level combined with mathematical modeling and the ability to vary the ligand concentration and gradients locally using microfluidic devices allowed us to separate the unique contributions of ligand concentration and ligand gradient to cell motility...
August 11, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28799592/rapid-determination-of-the-tumour-stroma-ratio-in-squamous-cell-carcinomas-with-desorption-electrospray-ionization-mass-spectrometry-desi-ms-a-proof-of-concept-demonstration
#16
Michael Woolman, Alessandra Tata, Delaram Dara, Jalna Meens, Elisa D'Arcangelo, Consuelo J Perez, Shamina Saiyara Prova, Emma Bluemke, Howard J Ginsberg, Demian Ifa, Alison McGuigan, Laurie Ailles, Arash Zarrine-Afsar
Squamous cell carcinomas constitute a major class of head & neck cancers, where the tumour stroma ratio (TSR) carries prognostic information. Patients affected by stroma-rich tumours exhibit a poor prognosis and a higher chance of relapse. As such, there is a need for a technology platform that allows rapid determination of the tumour stroma ratio. In this work, we provide a proof-of-principle demonstration that Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) can be used to determine tumour stroma ratios...
August 11, 2017: Analyst
https://www.readbyqxmd.com/read/28798946/ex-vivo-ooplasmic-extract-from-developing-drosophila-oocytes-for-quantitative-tirf-microscopy-analysis
#17
Imre Gaspar, Anne Ephrussi
Understanding the dynamic behavior and the continuously changing composition of macromolecular complexes, subcellular structures and organelles is one of areas of active research in both cell and developmental biology, as these changes directly relate to function and subsequently to the development and homeostasis of the organism. Here, we demonstrate the use of the developing Drosophila oocyte to study dynamics of messenger ribonucleoprotein complexes (mRNPs) with high spatiotemporal resolution. The combination of Drosophila genetics with total internal reflection (TIRF) microscopy, image processing and data analysis gives insight into mRNP motility and composition dynamics with unprecedented precision...
July 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28798525/bias-in-image-analysis-and-its-solution-unbiased-stereology
#18
REVIEW
Danielle L Brown
Although the human eye is excellent for pattern recognition, it often lacks the sensitivity to detect subtle changes in particle density. Because of this, quantitative evaluation may be required in some studies. A common type of quantitative assessment used for routine toxicology studies is two-dimensional histomorphometry. Although this technique can provide additional information about the tissue section being examined, it does not give information about the tissue as a whole. Furthermore, it produces biased (inaccurate) data that does not take into account the size, shape, or orientation of particles...
July 2017: Journal of Toxicologic Pathology
https://www.readbyqxmd.com/read/28798328/directional-cell-expansion-requires-nima-related-kinase-6-nek6-mediated-cortical-microtubule-destabilization
#19
Shogo Takatani, Shinichiro Ozawa, Noriyoshi Yagi, Takashi Hotta, Takashi Hashimoto, Yuichiro Takahashi, Taku Takahashi, Hiroyasu Motose
Plant cortical microtubules align perpendicular to the growth axis to determine the direction of cell growth. However, it remains unclear how plant cells form well-organized cortical microtubule arrays in the absence of a centrosome. In this study, we investigated the functions of Arabidopsis NIMA-related kinase 6 (NEK6), which regulates microtubule organization during anisotropic cell expansion. Quantitative analysis of hypocotyl cell growth in the nek6-1 mutant demonstrated that NEK6 suppresses ectopic outgrowth and promotes cell elongation in different regions of the hypocotyl...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797222/genetic-architecture-and-temporal-patterns-of-biomass-accumulation-in-spring-barley-revealed-by-image-analysis
#20
Kerstin Neumann, Yusheng Zhao, Jianting Chu, Jens Keilwagen, Jochen C Reif, Benjamin Kilian, Andreas Graner
BACKGROUND: Genetic mapping of phenotypic traits generally focuses on a single time point, but biomass accumulates continuously during plant development. Resolution of the temporal dynamics that affect biomass recently became feasible using non-destructive imaging. RESULTS: With the aim to identify key genetic factors for vegetative biomass formation from the seedling stage to flowering, we explored growth over time in a diverse collection of two-rowed spring barley accessions...
August 10, 2017: BMC Plant Biology
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