Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy
We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accura...
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| Veröffentlicht in: | Journal of biomedical optics Jg. 17; H. 12; S. 126008 |
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| Sprache: | Englisch |
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01.12.2012
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| Abstract | We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular design, Localizer can be readily extended with new algorithms as they become available, while maintaining the same interface and performance. We provide front-ends for running Localizer from Igor Pro, Matlab, or as a stand-alone program. We show that Localizer performs favorably when compared with two existing superresolution packages, and to our knowledge is the only freely available implementation of SOFI/pcSOFI microscopy. By dramatically improving the analysis performance and ensuring the easy addition of current and future enhancements, Localizer strongly improves the usability of superresolution imaging in a variety of biomedical studies. |
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| AbstractList | We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular design, Localizer can be readily extended with new algorithms as they become available, while maintaining the same interface and performance. We provide front-ends for running Localizer from Igor Pro, Matlab, or as a stand-alone program. We show that Localizer performs favorably when compared with two existing superresolution packages, and to our knowledge is the only freely available implementation of SOFI/pcSOFI microscopy. By dramatically improving the analysis performance and ensuring the easy addition of current and future enhancements, Localizer strongly improves the usability of superresolution imaging in a variety of biomedical studies.We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular design, Localizer can be readily extended with new algorithms as they become available, while maintaining the same interface and performance. We provide front-ends for running Localizer from Igor Pro, Matlab, or as a stand-alone program. We show that Localizer performs favorably when compared with two existing superresolution packages, and to our knowledge is the only freely available implementation of SOFI/pcSOFI microscopy. By dramatically improving the analysis performance and ensuring the easy addition of current and future enhancements, Localizer strongly improves the usability of superresolution imaging in a variety of biomedical studies. We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular design, Localizer can be readily extended with new algorithms as they become available, while maintaining the same interface and performance. We provide front-ends for running Localizer from Igor Pro, Matlab, or as a stand-alone program. We show that Localizer performs favorably when compared with two existing superresolution packages, and to our knowledge is the only freely available implementation of SOFI/pcSOFI microscopy. By dramatically improving the analysis performance and ensuring the easy addition of current and future enhancements, Localizer strongly improves the usability of superresolution imaging in a variety of biomedical studies. |
| Author | Duwé, Sam Zhang, Jin Dedecker, Peter Neely, Robert K |
| Author_xml | – sequence: 1 givenname: Peter surname: Dedecker fullname: Dedecker, Peter email: peter.dedecker@hotmail.com organization: The Johns Hopkins University School of Medicine, Department of Pharmacology and Molecular Sciences, 725 N. Wolfe Street, Baltimore, Mayland 21205, USA. peter.dedecker@hotmail.com – sequence: 2 givenname: Sam surname: Duwé fullname: Duwé, Sam – sequence: 3 givenname: Robert K surname: Neely fullname: Neely, Robert K – sequence: 4 givenname: Jin surname: Zhang fullname: Zhang, Jin |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23208219$$D View this record in MEDLINE/PubMed |
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| References | 18604216 - Nat Methods. 2008 Aug;5(8):687-94 18794861 - Nat Methods. 2008 Nov;5(11):943-5 20364147 - Nat Methods. 2010 May;7(5):377-81 16902090 - Science. 2006 Sep 15;313(5793):1642-5 20055915 - J Microsc. 2010 Jan;237(1):12-22 16896339 - Nat Methods. 2006 Oct;3(10):793-5 19890928 - Angew Chem Int Ed Engl. 2009;48(49):9285-9 20431545 - Nat Methods. 2010 May;7(5):339-40 17525330 - Science. 2007 May 25;316(5828):1153-8 21838238 - Nano Lett. 2011 Sep 14;11(9):4008-11 20483991 - Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10484-9 16980368 - Biophys J. 2006 Dec 1;91(11):4258-72 20018714 - Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22287-92 22711840 - Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10909-14 11964263 - Biophys J. 2002 May;82(5):2775-83 |
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| Title | Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy |
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