Extended Data Fig. 4: Incorporating refractive index mismatch aberrations in the estimated PSF model.
Bead data at different imaging depth were collected by imaging beads in agarose gel at stage positions from −1 µm to 5 µm, with a step size of 20 nm. Bead data at the coverslip were collected at stage positions from −1.5 µm to 1.5 µm, with a step size of 10 nm. (a) Localization of beads in agarose gel using the PSF model estimated from beads at the coverslip. (b) Localization of beads in agarose gel using the PSF model estimated from beads at the coverslip and modified by adding an index mismatch aberration at the estimated imaging depth of each bead. Therefore, each bead stack was localized by its own modified PSF model. Depth is defined as the estimated emitter’s z position to the coverslip. The z/x/y bias vs. z are defined as in SI Note 2 Eqs. 2.37 and 2.38. (c) Comparison of the PSF model at the coverslip, bead data at different imaging depth and their corresponding PSF models. With increasing depth, the pupil size slightly decreases as the effective numerical aperture (NA) decreases from 1.43 to 1.33 (the refractive index of water), and the pupil phase shows larger spherical aberration kind of patterns. Scale bars, 1 µm (c).
