Z-stage scanning

To extend the axial field of view in 3D SMLM experiments, data can be acquired in multiple z-stage positions [1]. However, the astigmatism method can estimate only the relative axial positions of molecules with respect to the focal plane. To find the absolute z coordinates, the correct offset must be added to the axial positions of each molecule. The new z coordinate can be determined as

z_{\mathrm{abs}}=z_{0}+z_{\mathrm{rel}}+z_{\mathrm{step}}\left(\left\lfloor%
\frac{f-1}{n_{\mathrm{im}}}\right\rfloor\bmod n_{\mathrm{pos}}\right)\,,

where z_{0} is the initial z-stage offset, z_{\mathrm{rel}} is the estimated molecular position relative to the focal plane (z_{\mathrm{rel}}=0 for 2D data), z_{\mathrm{step}} is the step between two positions of the Z-stage, f is the image frame in which a given molecule appeared, n_{\mathrm{im}} is the number of images taken in each z-stage position, and n_{\mathrm{pos}} is the number of z-stage positions. All z variables are in nm.

References

  • [1] B. Huang, S. A. Jones, B. Brandenburg and X. Zhuang(2008) Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution, Nature Methods 5 (12), pp. 1047–52. External Links: Document. Cited by: Z-stage scanning.