RT Journal Article
SR Electronic
T1 <em>PySOFI</em>: an open source Python package for SOFI
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.10.16.464651
DO 10.1101/2021.10.16.464651
A1 Yuting Miao
A1 Shimon Weiss
A1 Xiyu Yi
YR 2021
UL http://biorxiv.org/content/early/2021/10/16/2021.10.16.464651.abstract
AB 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 StatementThe authors have declared no competing interest.