Post on 14-Jan-2016
Beam Induced Movement and DDDs
Javier Vargas
Centro Nacional de Biotecnología-CSIC
jvargas@cnb.csic.es
The past…
The past…
Photographic film
Directly detects electrons
Good signal-to-noise performance (SNR)
Slow and laborious (films must be scanned, not possible automation)
The past…
Photographic film
Directly detects electrons
Good signal-to-noise performance (SNR)
Slow and laborious (films must be scanned, not possible automation)
CCD detectors
Suitable for automation.
Detect photons not electrons, it is needed an scintillator (bad spatial resolution).
Bad signal-to-noise performance.
The present…
Direct-electron Detectors Devices (DDDs)
Directly detects electrons.
Suitable for automation.
Better signal-to-noise ratio than film.
The present…
The present…
•The amount of additional noise added by a detector is measured by its detective quantum efficiency (DQE)
•Ideally a detector would not add any noise and so have a DQE of 1 but all real detectors have values less than 1.
The present…
Direct-electron Detectors Devices (DDDs)
Directly detects electrons.
Suitable for automation.
Better signal-to-noise ratio than film.
Very fast acquisition (17-100s frames/second)
We can “see” how the particles behaves as a function of the dose!
The present…
Direct-electron Detectors Devices (DDDs)
Directly detects electrons.
Suitable for automation.
Better signal-to-noise ratio than film.
Very fast acquisition (17-100s frames/second)
We can “see” how the particles behaves as a function of the dose!
The particles move !!! Beam Induced Movement
The present…
The present…
The present…
Brilot, A.F., Chen, J.Z., Cheng, A., Pan, J., Harrison, S.C., Potter, C.S., Carragher, B., Henderson, R., and Grigorieff, N. (2012). Beam-induced motion of vitrified specimen on holey carbon film. J Struct Biol 177, 630-637.
The present…
Global correction [Li 2013] By frame correction [Bai 2013]
Line track correction [Scheres 2014]
Li et al., 2013•The alignment method consists in a pure drift correction approach with some local correction dividing each sub-frame area into 3 × 3 regions, and determining the local motion of each region.
Fast, converts each movie to an aligned micrograph: Simple connection with standard image processing workflows
Not the best option for pronounced local BIM movements
[Li 2013]
Bai et al., 2013 16 Frame average
8 Frame average
6 Frame average
4 Frame average
2 Frame average
Bai et al., 2013
Scheres, 2014
Accurate in correcting for local and global in-plane
BIM movements
Optical Flow
Fast and “standard” (converts each
movie to an aligned micrograph)
New Graphical Tool to characterize BIM
pattern
Abrishami et al., JSB, 2015
Abrishami et al., JSB, 2015
Abrishami et al., JSB, 2015