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2023-08-25T06:50:47Z

Created page with "== Citation == Bromberg, Raquel / Guo, Yirui / Borek, Dominika / Otwinowski, Zbyszek. CryoEM single particle reconstruction with a complex-valued particle stack. 2023. J. Str..."

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== Citation ==

Bromberg, Raquel / Guo, Yirui / Borek, Dominika / Otwinowski, Zbyszek. CryoEM single particle reconstruction with a complex-valued particle stack. 2023. J. Structural Biology, Vol. 215, No. 2, p. 107945

== Abstract ==

Single particle reconstruction (SPR) in cryoEM is an image processing task with an elaborate hierarchy that starts
with many very noisy multi-frame images. Efficient representation of the intermediary image structures is critical
for keeping the calculations manageable. One such intermediary structure is called a particle stack and contains
cut-out images of particles in square boxes of predefined size. The micrograph that is the source of the boxed
images is usually corrected for motion between frames prior to particle stack creation. However, the contrast
transfer function (CTF) or its Fourier Transform point spread function (PSF) are not considered at this step.
Historically, the particle stack was intended for large particles and for a tighter PSF, which is characteristic of
lower resolution data. The field now performs analyses of smaller particles and to higher resolution, and these
conditions result in a broader PSF that requires larger padding and slower calculations to integrate information
for each particle. Consequently, the approach to handling structures such as the particle stack should be reexamined
to optimize data processing.
Here we propose to use as a source image for the particle stack a complex-valued image, in which CTF
correction is implicitly applied as a real component of the image. We can achieve it by applying an initial CTF
correction to the entire micrograph first and perform box cutouts as a subsequent step. The final CTF correction
that we refine and apply later has a very narrow PSF, and so cutting out particles from micrographs that were
approximately corrected for CTF does not require extended buffering, i.e. the boxes during the analysis only have
to be large enough to encompass the particle. The Fourier Transform of an exit-wave reconstruction creates an
image that has complex values. This is a complex value image considered in real space, opposed to standard SPR
data processing where complex numbers appear only in Fourier space. This extension of the micrograph concept
provides multiple advantages because the particle box size can be small and calculations crucial for high resolution
reconstruction such as Ewald sphere correction, aberration refinement, and particle-specific defocus
refinement can be performed on the small box data.

== Keywords ==

== Links ==

https://www.sciencedirect.com/science/article/pii/S1047847723000084

== Related software ==

== Related methods ==

== Comments ==

2023Bromberg Complex - Revision history

WikiSysop: Created page with "== Citation == Bromberg, Raquel / Guo, Yirui / Borek, Dominika / Otwinowski, Zbyszek. CryoEM single particle reconstruction with a complex-valued particle stack. 2023. J. Str..."