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Look@NanoSIMS - a tool for the analysis of nanoSIMS data in environmental microbiology.

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Title: Look@NanoSIMS - a tool for the analysis of nanoSIMS data in environmental microbiology.
Authors: Polerecky, Lubos1, Adam, Birgit1, Milucka, Jana1, Musat, Niculina1, Vagner, Tomas1, Kuypers, Marcel M. M.1
Source: Environmental Microbiology. Apr2012, Vol. 14 Issue 4, p1009-1023. 15p. 1 Color Photograph, 3 Charts, 3 Graphs.
Subjects: Microbial ecology, Open source software, Microbiology, Fluorescence in situ hybridization, Secondary ion mass spectrometry, Data analysis, Nanotechnology, Comparative studies, Computers in microbiology, Computer network resources
Abstract: Summary We describe an open-source freeware programme for high throughput analysis of nanoSIMS (nanometre-scale secondary ion mass spectrometry) data. The programme implements basic data processing and analytical functions, including display and drift-corrected accumulation of scanned planes, interactive and semi-automated definition of regions of interest (ROIs), and export of the ROIs' elemental and isotopic composition in graphical and text-based formats. Additionally, the programme offers new functions that were custom-designed to address the needs of environmental microbiologists. Specifically, it allows manual and automated classification of ROIs based on the information that is derived either from the nanoSIMS dataset itself (e.g. from labelling achieved by halogen in situ hybridization) or is provided externally (e.g. as a fluorescence in situ hybridization image). Moreover, by implementing post-processing routines coupled to built-in statistical tools, the programme allows rapid synthesis and comparative analysis of results from many different datasets. After validation of the programme, we illustrate how these new processing and analytical functions increase flexibility, efficiency and depth of the nanoSIMS data analysis. Through its custom-made and open-source design, the programme provides an efficient, reliable and easily expandable tool that can help a growing community of environmental microbiologists and researchers from other disciplines process and analyse their nanoSIMS data. [ABSTRACT FROM AUTHOR]
Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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PubType: Academic Journal
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  Data: Look@NanoSIMS - a tool for the analysis of nanoSIMS data in environmental microbiology.
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  Data: <searchLink fieldCode="JN" term="%22Environmental+Microbiology%22">Environmental Microbiology</searchLink>. Apr2012, Vol. 14 Issue 4, p1009-1023. 15p. 1 Color Photograph, 3 Charts, 3 Graphs.
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  Data: <searchLink fieldCode="DE" term="%22Microbial+ecology%22">Microbial ecology</searchLink><br /><searchLink fieldCode="DE" term="%22Open+source+software%22">Open source software</searchLink><br /><searchLink fieldCode="DE" term="%22Microbiology%22">Microbiology</searchLink><br /><searchLink fieldCode="DE" term="%22Fluorescence+in+situ+hybridization%22">Fluorescence in situ hybridization</searchLink><br /><searchLink fieldCode="DE" term="%22Secondary+ion+mass+spectrometry%22">Secondary ion mass spectrometry</searchLink><br /><searchLink fieldCode="DE" term="%22Data+analysis%22">Data analysis</searchLink><br /><searchLink fieldCode="DE" term="%22Nanotechnology%22">Nanotechnology</searchLink><br /><searchLink fieldCode="DE" term="%22Comparative+studies%22">Comparative studies</searchLink><br /><searchLink fieldCode="DE" term="%22Computers+in+microbiology%22">Computers in microbiology</searchLink><br /><searchLink fieldCode="DE" term="%22Computer+network+resources%22">Computer network resources</searchLink>
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  Data: Summary We describe an open-source freeware programme for high throughput analysis of nanoSIMS (nanometre-scale secondary ion mass spectrometry) data. The programme implements basic data processing and analytical functions, including display and drift-corrected accumulation of scanned planes, interactive and semi-automated definition of regions of interest (ROIs), and export of the ROIs' elemental and isotopic composition in graphical and text-based formats. Additionally, the programme offers new functions that were custom-designed to address the needs of environmental microbiologists. Specifically, it allows manual and automated classification of ROIs based on the information that is derived either from the nanoSIMS dataset itself (e.g. from labelling achieved by halogen in situ hybridization) or is provided externally (e.g. as a fluorescence in situ hybridization image). Moreover, by implementing post-processing routines coupled to built-in statistical tools, the programme allows rapid synthesis and comparative analysis of results from many different datasets. After validation of the programme, we illustrate how these new processing and analytical functions increase flexibility, efficiency and depth of the nanoSIMS data analysis. Through its custom-made and open-source design, the programme provides an efficient, reliable and easily expandable tool that can help a growing community of environmental microbiologists and researchers from other disciplines process and analyse their nanoSIMS data. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Environmental Microbiology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1111/j.1462-2920.2011.02681.x
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        Text: English
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      – SubjectFull: Open source software
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      – SubjectFull: Microbiology
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      – SubjectFull: Fluorescence in situ hybridization
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      – SubjectFull: Secondary ion mass spectrometry
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      – SubjectFull: Nanotechnology
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      – SubjectFull: Comparative studies
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      – SubjectFull: Computers in microbiology
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      – SubjectFull: Computer network resources
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      – TitleFull: Look@NanoSIMS - a tool for the analysis of nanoSIMS data in environmental microbiology.
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              Text: Apr2012
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