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GATE: software for the analysis and visualization of high-dimensional time series expression data

Ben D. MacArthur, Alexander Lachmann, Ihor R. Lemischka, Avi Ma'ayan
2009 Computer applications in the biosciences : CABIOS  
We present Grid Analysis of Time-series Expression (GATE), an integrated computational software platform for the analysis and visualization of high-dimensional bio-molecular time-series.  ...  GATE uses a correlation-based clustering algorithm to arrange molecular time-series on a two-dimensional hexagonal array and dynamically colors individual hexagons according to the expression level of  ...  ACKNOWLEDGEMENTS Thanks to Betty Chang, Dung-Fang Lee and Avinash Waghray for useful discussions.  ... 
doi:10.1093/bioinformatics/btp628 pmid:19892805 pmcid:PMC2796822 fatcat:dkt3inocxrd6xblbsle46pll74

Calcium Gating by the DHPR-RyR1 Pair

Montserrat Samso
2010 Biophysical Journal  
We propose a series of new modeling and analysis techniques, tailored towards handling of heteroneous data sets -heterogeneous in size, level of detail, resolution and conformation.  ...  The size and complexity of the multi-scale data sets is extremely diverse and demands novel strategies not only for the modeling approaches but also regarding pre-and post-processing and visualization.  ...  We propose a series of new modeling and analysis techniques, tailored towards handling of heteroneous data sets -heterogeneous in size, level of detail, resolution and conformation.  ... 
doi:10.1016/j.bpj.2009.12.2068 fatcat:77n5cvrjsngqtnatjem4hgjgpy

Gating, enhanced gating, and beyond: information utilization strategies for motion management, applied to preclinical PET

Adam Leon Kesner, Galith Abourbeh, Eyal Mishani, Roland Chisin, Sagi Tshori, Nanette Freedman
2013 EJNMMI Research  
In this work, we aimed to advance recently emerging data-driven gating methods and introduce a new strategy for optimizing the four-dimensional data based on information contained in that data.  ...  The mean liver displacement was 3.25 mm for gated and 3.04 mm for gating+ images.  ...  Acknowledgements We wish to acknowledge the Fulbright commission for Israel and the United States-Israel Educational Foundation which provided partial funding and support for this project.  ... 
doi:10.1186/2191-219x-3-29 pmid:23618039 pmcid:PMC3648448 fatcat:kzv3xgojyzejdihfeosgeowld4

Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses

Shadi Toghi Eshghi, Amelia Au-Yeung, Chikara Takahashi, Christopher R. Bolen, Maclean N. Nyachienga, Sean P. Lear, Cherie Green, W. Rodney Mathews, William E. O'Gorman
2019 Frontiers in Immunology  
While this approach has obvious potential for data visualization it remains unclear how t-SNE analysis compares to conventional manual hand-gating in stratifying and quantitating the frequency of diverse  ...  Dimensionality reduction using the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm has emerged as a popular tool for visualizing high-parameter single-cell data.  ...  ACKNOWLEDGMENTS We would like to acknowledge the contributions of the Genentech Core Biophysical Characterization and Reagent Facility including Mehraban Kosraviani, Bartek Bossak, Justin Low, Paul Vu,  ... 
doi:10.3389/fimmu.2019.01194 pmid:31231371 pmcid:PMC6560168 fatcat:x4d2uxlppvetljo2w6leqmlzdy

Compressed gated range sensing

Grigorios Tsagkatakis, Arnaud Woiselle, George Tzagkarakis, Marc Bousquet, Jean Luc Starck, Panagiotis Tsakalides, Dimitri Van De Ville, Vivek K. Goyal, Manos Papadakis
2013 Wavelets and Sparsity XV  
The CGRS technique employs a random gating function along with state-of-the-art reconstruction in order to estimate the timing of a returning laser pulse and infer the depth map.  ...  One of the most successful ARI techniques employs Time-of-Flight (ToF) cameras which emit and subsequently record laser pulses in order to estimate the distance between the camera and objects in a scene  ...  M. and Bacher, E., "Image coding for three-dimensional range-gated imaging," Applied Optics 50(21), 3824-3828 (2011).  ... 
doi:10.1117/12.2023901 fatcat:chddwi4cwfeypjfinnfn7twm4a

High-Throughput Analysis of Clinical Flow Cytometry Data by Automated Gating

Hunjoong Lee, Yongliang Sun, Lisa Patti-Diaz, Michael Hedrick, Anka G Ehrhardt
2019 Bioinformatics and Biology Insights  
Traditional manual gating is resource intense and becomes a bottleneck and an impractical method to complete high volumes of flow cytometry data analysis.  ...  However, for high-volume, complex flow cytometry data generated in clinical trials, conventional manual gating remains the standard of practice.  ...  for manual gating.  ... 
doi:10.1177/1177932219838851 pmid:30983860 pmcid:PMC6448119 fatcat:jeagfqdyinaqjacumny55zewyy

An Introduction to Automated Flow Cytometry Gating Tools and Their Implementation

Chris P. Verschoor, Alina Lelic, Jonathan L. Bramson, Dawn M. E. Bowdish
2015 Frontiers in Immunology  
For the second FlowCap competition, a series of software packages were tested for their ability to stratify a cohort of individuals into different classification groups based on their FCM data.  ...  The fluorescent dyes are then excited by the laser, and their emitted spectrum is detected by sensors, which digitize the information and visualizes it as two-dimensional dot plots, or one-dimensional  ...  Copyright © 2015 Verschoor, Lelic, Bramson and Bowdish. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).  ... 
doi:10.3389/fimmu.2015.00380 pmid:26284066 pmcid:PMC4515551 fatcat:bf4acu3sgjbmrgwlwbovllhq7e

flowClust: a Bioconductor package for automated gating of flow cytometry data

Kenneth Lo, Florian Hahne, Ryan R Brinkman, Raphael Gottardo
2009 BMC Bioinformatics  
This is a time-consuming task that ignores the high-dimensionality of FCM data.  ...  Nevertheless, there is an increasing concern about the lack of appropriate software tools to provide an automated analysis platform to parallelize the high-throughput data-generation platform.  ...  Acknowledgements The authors thank Martin Morgan, Patrick Aboyoun and Marc Carlson for their advice on the technical issues of building the flowClust package, and the two reviewers for suggestions that  ... 
doi:10.1186/1471-2105-10-145 pmid:19442304 pmcid:PMC2701419 fatcat:e3wceqxg6ndf5g5yfz6jhzmuui

Management Of Cultural Heritage: Bologna Gates

A. Ippolito, C. Bartolomei
2015 Zenodo  
The development and perfecting of techniques for acquiring and elaborating photorealistic 3D models, made them pivotal elements for popularizing information of objects on the scale of architectonic structures  ...  A growing demand is felt today for realistic 3D models enabling the cognition and popularization of historical-artistic heritage.  ...  They make use of the potentialities inherent in mobile devices, like for example restitution of high definition contents, and hence are Construction of the numeric model: this results in a three dimensional  ... 
doi:10.5281/zenodo.1109895 fatcat:hgbc3k7fq5bujkfinqnqwzn4cy

High temporal resolution OCT using image-based retrospective gating

Madhusudhana Gargesha, Michael W. Jenkins, David L. Wilson, Andrew M. Rollins
2009 Optics Express  
The gating technique employs image similarity measures for rearranging asynchronously acquired input data consisting of a time series of 2D images at each z position along the heart volume, to produce  ...  This gating method has allowed, for the first time, clear visualization of systolic dynamics of the looping embryonic heart in 3D.  ...  The authors also acknowledge James G. Fujimoto, Desmond Adler and Robert Huber for their technical contributions with the FDML laser.  ... 
doi:10.1364/oe.17.010786 pmid:19550478 pmcid:PMC2748662 fatcat:o3sgzsft2rhgnomgy4z4zakhpu

Sialic Acids Attached toO-Glycans Modulate Voltage-gated Potassium Channel Gating

Tara A. Schwetz, Sarah A. Norring, Andrew R. Ednie, Eric S. Bennett
2010 Journal of Biological Chemistry  
Neuronal, cardiac, and skeletal muscle action potentials are produced and conducted through the highly regulated activity of several types of voltage-gated ion channels.  ...  N-Linked sialic acids cannot be responsible for the G-V shifts because K v 4.2 and K v 4.3 cannot be N-glycosylated, and immunoblot analysis confirmed K v 2.1 is not N-glycosylated.  ...  Glycosidase gel shift data were analyzed using the Quantity One one-dimensional gel analysis software (Bio-Rad), as described previously (32) .  ... 
doi:10.1074/jbc.m110.171322 pmid:21115483 pmcid:PMC3039321 fatcat:nf2nevbn75civdf633wxng5p3a

Gate Set Tomography [article]

Erik Nielsen, John King Gamble, Kenneth Rudinger, Travis Scholten, Kevin Young, Robin Blume-Kohout
2021 arXiv   pre-print
In this paper, we cover GST's intellectual history, the techniques and experiments used to achieve its intended purpose, data analysis, gauge freedom and fixing, error bars, and the interpretation of gauge-fixed  ...  Long sequence GST can estimate gates with very high precision and efficiency, achieving Heisenberg scaling in regimes of practical interest.  ...  What's happening here is simple: the high-dimensional information contained in the data (1l and P k ) has to be compressed into the lower-dimensional space of the estimate G k .  ... 
arXiv:2009.07301v2 fatcat:aqnjp4xb4nhiboxwsx5wrxkusy

Gate Set Tomography

Erik Nielsen, John King Gamble, Kenneth Rudinger, Travis Scholten, Kevin Young, Robin Blume-Kohout
2021 Quantum  
In this paper, we cover GST's intellectual history, the techniques and experiments used to achieve its intended purpose, data analysis, gauge freedom and fixing, error bars, and the interpretation of gauge-fixed  ...  Long sequence GST can estimate gates with very high precision and efficiency, achieving Heisenberg scaling in regimes of practical interest.  ...  What's happening here is simple: the high-dimensional information contained in the data (1l and P k ) has to be compressed into the lower-dimensional space of the estimate G k .  ... 
doi:10.22331/q-2021-10-05-557 fatcat:liiywxtjwbgxjjhmpjvrn23dwq

Myocardial wall thickening from gated magnetic resonance images using Laplace's equation

M. Prasad, A. Ramesh, P. Kavanagh, J. Gerlach, G. Germano, D. S. Berman, P. J. Slomka, Maryellen L. Giger, Nico Karssemeijer
2009 Medical Imaging 2009: Computer-Aided Diagnosis  
Multiple slices of the myocardium in short-axis orientation at end-diastolic and endsystolic phases were considered for this analysis.  ...  For segmental analysis, we obtained an overall correlation of −0.55 (p<0.0001) with higher agreement along the mid and apical regions (r=−0.6).  ...  image analysis software.  ... 
doi:10.1117/12.811411 pmid:20835373 pmcid:PMC2936492 dblp:conf/micad/PrasadRKGGBS09 fatcat:iu3xqeeddfbwjegplnc6u4ir7a

Four-Dimensional Image Reconstruction Strategies in Cardiac-Gated and Respiratory-Gated PET Imaging

Arman Rahmim, Jing Tang, Habib Zaidi
2013 PET Clinics  
The development of advanced 4D physical anthropomorphic phantoms and computational models will benefit research in cardiac-gated and respiratory-gated PET imaging.  ...  A wide-ranging choice of techniques are available in research settings but have not yet been used in the clinic.  ...  There seems to be a general trend toward the use of increasingly sophisticated software for 4D reconstruction in cardiac-gated and respiratory-gated PET imaging.  ... 
doi:10.1016/j.cpet.2012.10.005 pmid:27157815 fatcat:wfqcow3fnnfv7pt2jg4i66fotq
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