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An abstract virtual instrument system for high throughput automatic microscopy

A.B.M. Russel, David Abramson, Blair Bethwaite, Minh Ngoc Dinh, Colin Enticott, Stephen Firth, Slavisa Garic, Ian Harper, Martin Lackmann, Stefan Schek, Mary Vail
2010 Procedia Computer Science  
We show that an AVI can be implemented using existing scientific workflow tools that both control the microscope and perform image analysis operations.  ...  The resulting solution is a flexible and powerful system for performing dynamic high throughput automatic microscopy.  ...  Acknowledgement This research is supported by an Australian Research Council (ARC) Linkage grant fostering collaboration between Monash University and Leica Microsystems.  ... 
doi:10.1016/j.procs.2010.04.058 fatcat:3vz4zh7efze23jznxi5p3eho6i

Industry News – March 2021

2021 Microscopy Today  
ParticleScout won second place in the category Spectroscopy and Microscopy. This award celebrates outstanding innovation in equipment used for scientific analysis.  ...  ZEISS html Seiwa Optical has Introduced Virtual Booth Seiwa Optical has created a virtual booth.  ... 
doi:10.1017/s1551929521000067 fatcat:qufddmft5bcenm6ctwf2i7fdim

Correlative Light and Volume Electron Microscopy (vCLEM): How Community Participation Can Advance Developing Technologies

Christopher J. Guerin, Saskia Lippens
2021 Journal of Microscopy  
While studies using this technique have been available since the 1960s, recent developments have enabled applying these workflows to large volumes of cells and tissues.  ...  Correlative light and electron microscopy is a valuable tool to image samples across resolution scales and link data on structure and function.  ...  used in the vCLEM workflow.  ... 
doi:10.1111/jmi.13056 pmid:34476818 pmcid:PMC9291772 fatcat:zlhh3uzpbndihfmodznrxym2xi

Towards Reproducibility of Microscopy Experiments

Sheeba Samuel, Frank Taubert, Daniel Walther, Birgitta König-Ries, H. Martin Bücker
2017 D-Lib Magazine  
"Virtual microscopy and analysis using scientific workflows." In: P roceedings Fifth IEEE International Conference on e-Science , 2009.  ...  The work demonstrates the use of scientific workflow systems in specifying and executing the environment.  ... 
doi:10.1045/january2017-samuel fatcat:nmbbqgzu25gqtlqzljszptbz6u

New Products

2013 Science  
Using light microscopy alone, images of biological matter smaller than 250 nm appear blurred and, as a result, are virtually impossible to analyze.  ...  several additional application modules as well as customer requested tools designed to increase the quality and speed of their NGS analysis workflow.  ... 
doi:10.1126/science.340.6130.382-a fatcat:yrpyqn4bdnbujaqilizf47pqwe

Internet of Things Architecture for High Throughput Biology [article]

David F. Parks, Kateryna Voitiuk, Jinghui Geng, Matthew A. T. Elliott, Matthew G. Keefe, Erik A. Jung, Ash Robbins, Pierre V. Baudin, Victoria T Ly, Nico Hawthorne, Dylan Yong, Sebastian E. Sanso (+9 others)
2021 bioRxiv   pre-print
A massively scalable and cost efficient platform for tissue experiments would benefit genomics, neuroscience, and translational medicine by enabling advanced high throughput tissue screens.  ...  However, these cell culture experiments are restricted by high costs and limited labor.  ...  .), the National Defense Science and Engineering Graduate Fellowship (00002116, M.G.K.), and a gift the William K. Bowes Jr Foundation (T.J.N).  ... 
doi:10.1101/2021.07.29.453595 fatcat:ou3fsy5mxjdqtcjzy5bysiznle

A Correlative Imaging Approach for Extracellular Matrix Characterization in Mice

Yifei Liu, Yong-Ung Lee, Tai Yi, Ken Wu, Cedric Bouchet-Marquis, Han Chan, Christopher K. Breuer, David W. McComb
2019 Microscopy and Microanalysis  
Fig. 1A shows an example volume rendering from Avizo image processing and data analysis software (Thermo Fisher Scientific) and a virtual slice along the major axis 1134  ...  We propose a correlative workflow utilizing microcomputed tomography (µCT), scanning electron microscopy (SEM) in combination with serial block face imaging (SBFI) and transmission electron microscopy  ...  Fig. 1A shows an example volume rendering from Avizo image processing and data analysis software (Thermo Fisher Scientific) and a virtual slice along the major axis of the pulmonary artery, Fig 1B.  ... 
doi:10.1017/s1431927619006408 fatcat:inppp7m5gjadnjj35mdse4wrfm

Introduction of virtual microscopy in routine surgical pathology - a hypothesis and personal view from Europe

Klaus Kayser
2012 Diagnostic Pathology  
The technology of whole image acquisition from histological glass slides (Virtual slides, (VS)) and its associated software such as image storage, viewers, and virtual microscopy (VM), has matured in the  ...  Virtual Slides: The virtual slide(s) for this article can be found here:  ...  Digital pathology and tissue-based diagnosis The acquisition of virtual slides and associated virtual microscopy (VM) to interpret digital images occur close to the end of the diagnostic chain, typically  ... 
doi:10.1186/1746-1596-7-48 pmid:22546238 pmcid:PMC3441330 fatcat:vcsatxve6bdaxhmvrxiuafcewy

PathGrid: a service-orientated architecture for microscopy image analysis

N. A. Walton, J. D. Brenton, C. Caldas, M. J. Irwin, A. Akram, E. Gonzalez-Solares, J. R. Lewis, P. H. Maccallum, L. J. Morris, G. T. Rixon
2010 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
and workflow management, and astronomical image analysis software adapted for the analysis of high-throughput astronomy imaging surveys.  ...  This paper describes 'PathGrid'-an analysis and data integration system, developed initially to meet the demands in the analysis of medical microscopy imaging data.  ...  This is a powerful virtual research environment that makes it easy to find, use and share scientific workflows, and thus will provide a useful underpinning 'sharing' technology for the growing numbers  ... 
doi:10.1098/rsta.2010.0158 pmid:20643686 fatcat:63clp6mcfjgafomyiutihwjvpq

Game-Engine-Assisted Research platform for Scientific computing (GEARS) in Virtual Reality

Brandon K. Horton, Rajiv K. Kalia, Erick Moen, Aiichiro Nakano, Ken-ichi Nomura, Michael Qian, Priya Vashishta, Anders Hafreager
2019 SoftwareX  
GEARS also features a novel data exploration tool called virtual confocal microscopy, which endows scientific visualization with enhanced functionality.  ...  simulations and on-the-fly data exploration in virtual reality (VR) environments.  ...  Using our workflow, outlined above, and our provided vertex shader, one can apply 3D virtual confocal microscopy to any discrete data set.  ... 
doi:10.1016/j.softx.2019.01.009 fatcat:6exr2lvwuffahgbrbtqmvfs2fe

Processing Volumetric Data for Correlative Analysis: An Anecdote from a Core Facility

Connon I. Thomas, Naomi Kamasawa
2019 Microscopy and Microanalysis  
Image processing and analysis are complicated, with countless algorithms and programs available to perform any one step of the pipeline [1].  ...  Each must be performed carefully yet efficiently to result in a useful and interpretable output.  ...  In summary, this paper hopes to serve three purposes: 1) describe an example workflow that we used to process and output useful biological data; 2) encourage conversation of already available data analysis  ... 
doi:10.1017/s1431927619007645 fatcat:yin3dulvxvdijd6aifjsqk5bny

IMP Science Gateway: from the Portal to the Hub of Virtual Experimental Labs in Materials Science [article]

Yuri Gordienko, Lev Bekenev, Olexandra Baskova, Olexander Gatsenko, Elena Zasimchuk, Sergii Stirenko
2014 arXiv   pre-print
The typical scientific workflows with possible scenarios of its preparation and usage are presented.  ...  Several typical use cases for these science applications (scientific workflows) are considered for molecular dynamics (MD) simulations of complex behavior of various nanostructures (nanoindentation of  ...  Each simulation workflow can be considered as a virtual counterpart (virtual lab) of the real experimental process, and the SG itself can be used as a hub of such virtual experimental labs in materials  ... 
arXiv:1404.5611v1 fatcat:52d7dkft5rbe7fuxcbioajjgba

Report On Existing Metadata Standards, And Proposals For New Vocabularies

Chris Morris
2018 Zenodo  
increasing use of it, ... particularly for hybrid and integrative models, Recording provenance Linking datasets to research projects Adoption of CWL for describing workflows Metadata support in West-Life  ...  This report therefore plans practical steps to deliver improvements during remaining months of West-Life, and steps to enable future culture changes and implementation.  ...  Therefore partner CSIC is engaged in an EOSC Pilot Project 'CryoEM workflows: Linking distributed data and data analysis resources as workflows in Structural Biology with cryo Electron Microscopy: Interoperability  ... 
doi:10.5281/zenodo.1249378 fatcat:g5hb64rvyre23pouxxfehowasy

In situ Dynamic X-ray Tomography in the Laboratory

Arno Merkle, Marijn Boone, Denis Van Loo
2018 Microscopy and Microanalysis  
The methodology and dedicated workflow from acquisition through analysis is illustrated by way of example using fluid flow experiments performed in a custom-made Xray transparent flow cell on artificial  ...  time dimension in the 3D analysis workflow to improve image quality.  ...  The methodology and dedicated workflow from acquisition through analysis is illustrated by way of example using fluid flow experiments performed in a custom-made Xray transparent flow cell on artificial  ... 
doi:10.1017/s1431927618005482 fatcat:q4aoxelp65do7ec752moajfj5y

Industry News – Jan 2021

2021 Microscopy Today  
and workflow.  ...  The EDAX Octane Elite EDS Analysis System was used in conjunction with the Gatan Monarc CL detector to capture EDS, CL, and SEM signals of the mineral kyanite (Al 2 SiO 5 ) within the Gatan Microscopy  ... 
doi:10.1017/s1551929520001674 fatcat:kyytptzlnfdkbehpojdn6nwyva
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