MicroVIP: Microscopy image simulation on the Virtual Imaging Platform

MicroVIP is an open source software that assembles, in a unified web-application running on distributed computing resources, simulators of the main fluorescent microscopy imaging modalities (with existing codes or newly developed). MicroVIP provides realistic simulated images including several sourc...

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Autores principales:	Ali Ahmad, Guillaume Vanel, Sorina Camarasu-Pop, Axel Bonnet, Carole Frindel, David Rousseau
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Microscopy image simulation Virtual Imaging Platform Machine learning Computer software QA76.75-76.765
Acceso en línea:	https://doaj.org/article/444258291499420cab568f8059931f60
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spelling	oai:doaj.org-article:444258291499420cab568f8059931f602021-11-16T04:10:51ZMicroVIP: Microscopy image simulation on the Virtual Imaging Platform2352-711010.1016/j.softx.2021.100854https://doaj.org/article/444258291499420cab568f8059931f602021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S235271102100131Xhttps://doaj.org/toc/2352-7110MicroVIP is an open source software that assembles, in a unified web-application running on distributed computing resources, simulators of the main fluorescent microscopy imaging modalities (with existing codes or newly developed). MicroVIP provides realistic simulated images including several sources of noise (microfluidic blur effect, diffraction, Poisson noise, camera read out noise). MicroVIP also includes a module which simulates single cells with fluorescent markers and a module to analyze the simulated images with textural and pointillist feature spaces. MicroVIP is shown to be of value for supervised machine learning. It allow to automatically generate large sets of training images and virtual instrumentation to optimize the optical parameters before realizing real experiments.Ali AhmadGuillaume VanelSorina Camarasu-PopAxel BonnetCarole FrindelDavid RousseauElsevierarticleMicroscopy image simulationVirtual Imaging PlatformMachine learningComputer softwareQA76.75-76.765ENSoftwareX, Vol 16, Iss , Pp 100854- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microscopy image simulation Virtual Imaging Platform Machine learning Computer software QA76.75-76.765
spellingShingle	Microscopy image simulation Virtual Imaging Platform Machine learning Computer software QA76.75-76.765 Ali Ahmad Guillaume Vanel Sorina Camarasu-Pop Axel Bonnet Carole Frindel David Rousseau MicroVIP: Microscopy image simulation on the Virtual Imaging Platform
description	MicroVIP is an open source software that assembles, in a unified web-application running on distributed computing resources, simulators of the main fluorescent microscopy imaging modalities (with existing codes or newly developed). MicroVIP provides realistic simulated images including several sources of noise (microfluidic blur effect, diffraction, Poisson noise, camera read out noise). MicroVIP also includes a module which simulates single cells with fluorescent markers and a module to analyze the simulated images with textural and pointillist feature spaces. MicroVIP is shown to be of value for supervised machine learning. It allow to automatically generate large sets of training images and virtual instrumentation to optimize the optical parameters before realizing real experiments.
format	article
author	Ali Ahmad Guillaume Vanel Sorina Camarasu-Pop Axel Bonnet Carole Frindel David Rousseau
author_facet	Ali Ahmad Guillaume Vanel Sorina Camarasu-Pop Axel Bonnet Carole Frindel David Rousseau
author_sort	Ali Ahmad
title	MicroVIP: Microscopy image simulation on the Virtual Imaging Platform
title_short	MicroVIP: Microscopy image simulation on the Virtual Imaging Platform
title_full	MicroVIP: Microscopy image simulation on the Virtual Imaging Platform
title_fullStr	MicroVIP: Microscopy image simulation on the Virtual Imaging Platform
title_full_unstemmed	MicroVIP: Microscopy image simulation on the Virtual Imaging Platform
title_sort	microvip: microscopy image simulation on the virtual imaging platform
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/444258291499420cab568f8059931f60
work_keys_str_mv	AT aliahmad microvipmicroscopyimagesimulationonthevirtualimagingplatform AT guillaumevanel microvipmicroscopyimagesimulationonthevirtualimagingplatform AT sorinacamarasupop microvipmicroscopyimagesimulationonthevirtualimagingplatform AT axelbonnet microvipmicroscopyimagesimulationonthevirtualimagingplatform AT carolefrindel microvipmicroscopyimagesimulationonthevirtualimagingplatform AT davidrousseau microvipmicroscopyimagesimulationonthevirtualimagingplatform
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MicroVIP: Microscopy image simulation on the Virtual Imaging Platform

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