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quantitative image analysis

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https://www.readbyqxmd.com/read/27911372/quantitative-hardness-measurement-by-instrumented-afm-indentation
#1
Arnaud Caron
In this work, a combination of amplitude-modulated non-contact atomic force microscopy and atomic force spectroscopy is applied for instrumented hardness measurements on an Au(111) surface with atomistic resolution of single plasticity events. A careful experimental procedure is described that includes the force sensor selection, its calibration, the calibration of the cantilever deflection detection system, and the minimization of instrumental drift for accurate and reproducible force-distance measurements...
November 22, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911038/quantitating-the-cell-turning-images-into-numbers-with-imagej
#2
REVIEW
Ellen T Arena, Curtis T Rueden, Mark C Hiner, Shulei Wang, Ming Yuan, Kevin W Eliceiri
Modern biological research particularly in the fields of developmental and cell biology has been transformed by the rapid evolution of the light microscope. The light microscope, long a mainstay of the experimental biologist, is now used for a wide array of biological experimental scenarios and sample types. Much of the great developments in advanced biological imaging have been driven by the digital imaging revolution with powerful processors and algorithms. In particular, this combination of advanced imaging and computational analysis has resulted in the drive of the modern biologist to not only visually inspect dynamic phenomena, but to quantify the involved processes...
December 2, 2016: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/27910875/an-integrated-modelling-framework-from-cells-to-organism-based-on-a-cohort-of-digital-embryos
#3
Paul Villoutreix, Julien Delile, Barbara Rizzi, Louise Duloquin, Thierry Savy, Paul Bourgine, René Doursat, Nadine Peyriéras
We conducted a quantitative comparison of developing sea urchin embryos based on the analysis of five digital specimens obtained by automatic processing of in toto 3D+ time image data. These measurements served the reconstruction of a prototypical cell lineage tree able to predict the spatiotemporal cellular organisation of a normal sea urchin blastula. The reconstruction was achieved by designing and tuning a multi-level probabilistic model that reproduced embryo-level dynamics from a small number of statistical parameters characterising cell proliferation, cell surface area and cell volume evolution along the cell lineage...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910868/relationship-between-nanotopographical-alignment-and-stem-cell-fate-with-live-imaging-and-shape-analysis
#4
Peter Newman, Jorge Luis Galenano-Niño, Pamela Graney, Joselito M Razal, Andrew I Minett, João Ribas, Raquel Ovalle-Robles, Maté Biro, Hala Zreiqat
The topography of a biomaterial regulates cellular interactions and determine stem cell fate. A complete understanding of how topographical properties affect cell behavior will allow the rational design of material surfaces that elicit specified biological functions once placed in the body. To this end, we fabricate substrates with aligned or randomly organized fibrous nanostructured topographies. Culturing adipose-derived stem cells (ASCs), we explore the dynamic relationship between the alignment of topography, cell shape and cell differentiation to osteogenic and myogenic lineages...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910599/synthetic-plasma-edge-diagnostics-for-emc3-eirene-highlighted-for-wendelstein-7-x
#5
H Frerichs, F Effenberg, O Schmitz, C Biedermann, Y Feng, M Jakubowski, R König, M Krychowiak, J Lore, H Niemann, T S Pedersen, L Stephey, G A Wurden
Interpretation of spectroscopic measurements in the edge region of high-temperature plasmas can be a challenge since line of sight integration effects make direct interpretation in terms of quantitative, local emission strengths often impossible. The EMC3-EIRENE code-a 3D fluid edge plasma and kinetic neutral gas transport code-is a suitable tool for full 3D reconstruction of such signals. A versatile synthetic diagnostic module has been developed recently which allows the realistic 3D setup of various plasma edge diagnostics to be captured...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910407/anisotropic-contrast-optical-microscope
#6
D Peev, T Hofmann, N Kananizadeh, S Beeram, E Rodriguez, S Wimer, K B Rodenhausen, C M Herzinger, T Kasputis, E Pfaunmiller, A Nguyen, R Korlacki, A Pannier, Y Li, E Schubert, D Hage, M Schubert
An optical microscope is described that reveals contrast in the Mueller matrix images of a thin, transparent, or semi-transparent specimen located within an anisotropic object plane (anisotropic filter). The specimen changes the anisotropy of the filter and thereby produces contrast within the Mueller matrix images. Here we use an anisotropic filter composed of a semi-transparent, nanostructured thin film with sub-wavelength thickness placed within the object plane. The sample is illuminated as in common optical microscopy but the light is modulated in its polarization using combinations of linear polarizers and phase plate (compensator) to control and analyze the state of polarization...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910021/quantitative-fluorescence-in-situ-hybridization-qfish
#7
Ivan Y Iourov
Fluorescence in situ hybridization (FISH) has a wide spectrum of applications in current molecular cytogenetic and cancer research. This is a unique technique that can be used for chromosomal DNA analysis in all cell types, at all stages of the cell cycle, and at molecular resolution. Recent developments in microscopy and imaging systems have allowed quantification of digital FISH images (quantitative FISH or QFISH) and have provided a new way for molecular cytogenetic analysis at single-cell level. QFISH can be applied for studying chromosome imbalances in interphase nuclei or metaphase spreads, measuring relative DNA content at chromosomal loci and identifying parental origin of homologous chromosomes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909128/the-development-of-a-quantitative-scoring-system-to-predict-whether-a-large-to-massive-rotator-cuff-tear-can-be-arthroscopically-repaired
#8
S-J Kim, J-S Park, K-H Lee, B-G Lee
AIMS: The aim of the study was to develop a quantitative scoring system to predict whether a large-to-massive rotator cuff tear was arthroscopically reparable prior to surgery. PATIENTS AND METHODS: We conducted a retrospective review of the pre-operative MR imaging and surgical records of 87 patients (87 shoulders) who underwent arthroscopic repair of a large-to-massive rotator cuff tear. Patients were divided into two groups, based on the surgical outcome of the repair...
December 2016: Bone & Joint Journal
https://www.readbyqxmd.com/read/27908174/respiratory-motion-compensation-for-simultaneous-pet-mr-based-on-highly-undersampled-mr-data
#9
Christopher M Rank, Thorsten Heußer, Andreas Wetscherek, Martin T Freitag, Oliver Sedlaczek, Heinz-Peter Schlemmer, Marc Kachelrieß
PURPOSE: Positron emission tomography (PET) of the thorax region is impaired by respiratory patient motion. To account for motion, the authors propose a new method for PET/magnetic resonance (MR) respiratory motion compensation (MoCo), which uses highly undersampled MR data with acquisition times as short as 1 min/bed. METHODS: The proposed PET/MR MoCo method (4D jMoCo PET) uses radial MR data to estimate the respiratory patient motion employing MR joint motion estimation and image reconstruction with temporal median filtering...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27908165/a-comparison-of-two-prospective-risk-analysis-methods-traditional-fmea-and-a-modified-healthcare-fmea
#10
Jeong-Eun Rah, Ryan P Manger, Adam D Yock, Gwe-Ya Kim
PURPOSE: To examine the abilities of a traditional failure mode and effects analysis (FMEA) and modified healthcare FMEA (m-HFMEA) scoring methods by comparing the degree of congruence in identifying high risk failures. METHODS: The authors applied two prospective methods of the quality management to surface image guided, linac-based radiosurgery (SIG-RS). For the traditional FMEA, decisions on how to improve an operation were based on the risk priority number (RPN)...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27908157/volumetry-of-low-contrast-liver-lesions-with-ct-investigation-of-estimation-uncertainties-in-a-phantom-study
#11
Qin Li, Yongguang Liang, Qiao Huang, Min Zong, Benjamin Berman, Marios A Gavrielides, Lawrence H Schwartz, Binsheng Zhao, Nicholas Petrick
PURPOSE: To evaluate the performance of lesion volumetry in hepatic CT as a function of various imaging acquisition parameters. METHODS: An anthropomorphic abdominal phantom with removable liver inserts was designed for this study. Two liver inserts, each containing 19 synthetic lesions with varying diameter (6-40 mm), shape, contrast (10-65 HU), and both homogenous and mixed-density were designed to have background and lesion CT values corresponding to arterial and portal-venous phase imaging, respectively...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27908155/a-new-algorithm-for-estimating-the-rod-volume-fraction-and-the-trabecular-thickness-from-in-vivo-computed-tomography
#12
Felix Sebastian Leo Thomsen, Jaime Andrés Peña, Yongtao Lu, Gerd Huber, Michael Morlock, Claus-Christian Glüer, Claudio Augusto Delrieux
PURPOSE: Existing microstructure parameters are able to predict vertebral in vitro failure load, but for noisy in vivo data more complex algorithms are needed for a robust assessment. METHODS: A new algorithm is proposed for the microstructural analysis of trabecular bone under in vivo quantitative computed tomography (QCT). Five fractal parameters are computed: (1) the average local fractal dimension FD, (2) its standard deviation FD.SD, (3) the fractal rod volume ratio fRV/BV, (4) the average fractal trabecular thickness fTb...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27908020/tug-of-war-lacunarity-a-novel-approach-for-estimating-lacunarity
#13
Martin A Reiss, Birgit Lemmerer, Arnold Hanslmeier, Helmut Ahammer
Modern instrumentation provides us with massive repositories of digital images that will likely only increase in the future. Therefore, it has become increasingly important to automatize the analysis of digital images, e.g., with methods from pattern recognition. These methods aim to quantify the visual appearance of captured textures with quantitative measures. As such, lacunarity is a useful multi-scale measure of texture's heterogeneity but demands high computational efforts. Here we investigate a novel approach based on the tug-of-war algorithm, which estimates lacunarity in a single pass over the image...
November 2016: Chaos
https://www.readbyqxmd.com/read/27907861/in-situ-time-lapse-study-of-extracellular-polymeric-substance-discharge-in-streptococcus-mutans-biofilm
#14
Bernard Haochih Liu, Li-Chieh Yu
Streptococcus mutans is one of the main pathogens that cause tooth decay. By metabolizing carbohydrates, S. mutans emits extracellular polymeric substance (EPS) that adheres to the tooth surface and forms layers of biofilm. Periodontal disease occurs due to the low pH environment created by S. mutans biofilm, and such an acidic environment gradually erodes tooth enamel. Since the existence of EPS is essential in the formation of biofilm, the in-situ investigation of its generation and distribution in real time is the key to the control and suppression of S...
November 24, 2016: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/27907850/automated-annotation-and-quantitative-description-of-ultrasound-videos-of-the-fetal-heart
#15
Christopher P Bridge, Christos Ioannou, J Alison Noble
Interpretation of ultrasound videos of the fetal heart is crucial for the antenatal diagnosis of congenital heart disease (CHD). We believe that automated image analysis techniques could make an important contribution towards improving CHD detection rates. However, to our knowledge, no previous work has been done in this area. With this goal in mind, this paper presents a framework for tracking the key variables that describe the content of each frame of freehand 2D ultrasound scanning videos of the healthy fetal heart...
November 19, 2016: Medical Image Analysis
https://www.readbyqxmd.com/read/27907830/a-methodology-for-finding-the-optimal-iteration-number-of-the-sirt-algorithm-for-quantitative-electron-tomography
#16
Ana Okariz, Teresa Guraya, Maider Iturrondobeitia, Julen Ibarretxe
The SIRT (Simultaneous Iterative Reconstruction Technique) algorithm is commonly used in Electron Tomography to calculate the original volume of the sample from noisy images, but the results provided by this iterative procedure are strongly dependent on the specific implementation of the algorithm, as well as on the number of iterations employed for the reconstruction. In this work, a methodology for selecting the iteration number of the SIRT reconstruction that provides the most accurate segmentation is proposed...
November 19, 2016: Ultramicroscopy
https://www.readbyqxmd.com/read/27907065/statistical-frailty-modeling-for-quantitative-analysis-of-exocytotic-events-recorded-by-live-cell-imaging-rapid-release-of-insulin-containing-granules-is-impaired-in-human-diabetic-%C3%AE-cells
#17
Giuliana Cortese, Nikhil R Gandasi, Sebastian Barg, Morten Gram Pedersen
Hormones and neurotransmitters are released when secretory granules or synaptic vesicles fuse with the cell membrane, a process denoted exocytosis. Modern imaging techniques, in particular total internal reflection fluorescence (TIRF) microscopy, allow the investigator to monitor secretory granules at the plasma membrane before and when they undergo exocytosis. However, rigorous statistical approaches for temporal analysis of such exocytosis data are still lacking. We propose here that statistical methods from time-to-event (also known as survival) analysis are well suited for the problem...
2016: PloS One
https://www.readbyqxmd.com/read/27906811/measurement-of-radial-peripapillary-capillary-density-in-the-normal-human-retina-using-optical-coherence-tomography-angiography
#18
Tarannum Mansoori, Jayanthi Sivaswamy, Jahnavi Sai Gamalapati, Satish Gooty Agraharam, Nagalla Balakrishna
AIM: To image the radial peripapillary capillary (RPC) network with optical coherence tomography angiography (OCTA) and measure its capillary density (CD) in the normal human retina. MATERIALS AND METHODS: Fifty-two normal participants underwent OCTA imaging with RTVue XR 100 Avanti OCT. The angioflow enface RPCs network was extracted from OCTA and 8 peripapillary sectors with a sector angle of 45 degrees were selected for quantitative analysis: superior nasal, superior temporal, temporal upper, temporal lower, nasal upper, nasal lower, inferior nasal, and inferior temporal...
November 30, 2016: Journal of Glaucoma
https://www.readbyqxmd.com/read/27906190/robust-high-throughput-kinetic-analysis-of-apoptosis-with-real-time-high-content-live-cell-imaging
#19
Jesse D Gelles, Jerry Edward Chipuk
Quantitative and kinetic analyses of apoptotic cell death are integral components of exploring cell biology, measuring cellular stress responses, and performing high-throughput genomic/RNAi/drug screens. Here, we present a detailed method that integrates robust kinetic real-time high-content imaging with Annexin V labelling to provide a highly sensitive, accurate, simple and zero-handling approach to quantify extrinsic and intrinsic inducers of apoptosis. The sensitivity of this non-toxic method outperforms previous high-throughput methodologies using viability dyes or caspase-activation reporters...
December 1, 2016: Cell Death & Disease
https://www.readbyqxmd.com/read/27903193/three-dimensional-assessment-of-the-effects-of-high-density-embolization-material-on-the-absorbed-dose-in-the-target-for-gamma-knife-radiosurgery-of-arteriovenous-malformations
#20
Yoichi Watanabe, Divyajot Sandhu, Leighton Warmington, Sean Moen, Ramachandra Tummala
OBJECTIVE Arteriovenous malformation (AVM) is an intracranial vascular disorder. Gamma Knife radiosurgery (GKRS) is used in conjunction with intraarterial embolization to eradicate the nidus of AVMs. Clinical results indicate that patients with prior embolization tend to gain less benefit from GKRS. The authors hypothesized that this was partly caused by dosimetric deficiency. The actual dose delivered to the target may be smaller than the intended dose because of increased photon attenuation by high-density embolic materials...
December 2016: Journal of Neurosurgery
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