Characterization of polarization dependence in super-resolution fluorescent microscopy via phase retrieval
Résumé
In single molecule orientation localization microscopy, aberrations cause changes in the shape of the point spread function (PSF) generated by point-like dipolar sources, which can lead to an erroneous estimation of the source's position and orientation. A common strategy for addressing this issue is to model the aberrations as a scalar pupil phase mask and characterize them using a stack of PSFs for varying defocus using phase retrieval algorithms. However, this strategy fails when there are polarization-dependent aberrations, introduced either through unintentional anisotropy in the system or by using birefringent masks for PSF shaping. Here, a model and methodology for the proper characterization of polarization-dependent aberrations are introduced. The key components are the modeling of polarization aberrations via a spatially-dependent Jones matrix, commonly used to describe birefringent elements, and the introduction of polarization diversity for its correct estimation via a phase retrieval algorithm based on a nonlinear optimization. The software pyPSFstack used for the modeling and characterization is also made freely available.