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PySOFI: an open source Python package for SOFI

Yuting Miao, Shimon Weiss, Xiyu Yi
doi: https://doi.org/10.1101/2021.10.16.464651
Yuting Miao
1Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA
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  • For correspondence: ytmiao@ucla.edu
Shimon Weiss
1Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA
2Department of Physiology, University of California, Los Angeles 90095, US
3Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University,Ramat-Gan 52900, Israel
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  • For correspondence: sweiss@chem.ucla.edu
Xiyu Yi
4Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
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  • For correspondence: yi10@llnl.gov
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ABSTRACT

Super-resolution optical fluctuation imaging (SOFI) is a highly democratizable technique that provides optical super-resolution (SR) without requirement of sophisticated imaging instruments. An open source package for SOFI algorithm is needed to support not only the utilization of SOFI, but also the community adoption and participation for further development of SOFI. In this work, we developed PySOFI, an open source python package for SOFI analysis that offers the flexibility to inspect, test, modify, improve and extend the algorithm. We provide a complete documentation for the package and a collection of Jupyter Notebooks to demonstrate the usage of the package. We discuss the architecture of PySOFI, illustrate how to use each functional module, and demonstrate how to extend the PySOFI package with additional modules. We expect PySOFI to facilitate efficient adoption, testing, modification, dissemination and prototyping of new SOFI-relevant algorithms.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • The work from X. Yi was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Release number: LLNL-JRNL-827376

  • https://github.com/xiyuyi-at-LLNL/pysofi

  • https://figshare.com/s/47d97a2df930380c96bb

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 16, 2021.
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PySOFI: an open source Python package for SOFI
Yuting Miao, Shimon Weiss, Xiyu Yi
bioRxiv 2021.10.16.464651; doi: https://doi.org/10.1101/2021.10.16.464651
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PySOFI: an open source Python package for SOFI
Yuting Miao, Shimon Weiss, Xiyu Yi
bioRxiv 2021.10.16.464651; doi: https://doi.org/10.1101/2021.10.16.464651

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