Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform
Ruijie Cao, Yaning Li, Xin Chen, Xichuan Ge, Meiqi Li, Meiling Guan, Yiwei Hou, Yunzhe Fu, Xinzhu Xu, Christophe Leterrier, Shan Jiang, Baoxiang Gao, Peng Xi
Abstract
Open-3DSIM is an open-source reconstruction platform for three-dimensional structured illumination microscopy. We demonstrate its superior performance for artifact suppression and high-fidelity reconstruction relative to other algorithms on various specimens and over a range of signal-to-noise levels. Open-3DSIM also offers the capacity to extract dipole orientation, paving a new avenue for interpreting subcellular structures in six dimensions (xyzθλt). The platform is available as MATLAB code, a Fiji plugin and an Exe application to maximize user-friendliness.
Topics & Concepts
Computer scienceOpen sourceMicroscopyArtifact (error)Plug-inComputer visionOrientation (vector space)High fidelityFidelityCode (set theory)Source codeMATLABArtificial intelligenceComputer graphics (images)OpticsSoftwarePhysicsSet (abstract data type)Programming languageGeometryTelecommunicationsAcousticsMathematicsAdvanced Fluorescence Microscopy TechniquesAdvanced Electron Microscopy Techniques and ApplicationsDigital Holography and Microscopy