MotionCor2

Correction of electron beam-induced sample motion is one of the major factors contributing to the recent resolution breakthroughs in cryo-electron microscopy. Based on observations that the electron beam induces doming of the thin vitreous ice layer, we developed an algorithm to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. The multi-GPU accelerated program, MotionCor2, is sufficiently fast to keep up with automated data collection. The result is an exceptionally robust strategy that can work on a wide range of data sets, including those very close to focus or with very short integration times, obviating the need for particle polishing. Application significantly improves Thon ring quality and 3D reconstruction resolution.

Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy, Nature Methods, submitted. BioArxiv: http://biorxiv.org/content/early/2016/07/04/061960


UCSFImage4

UCSFImage4 is a program for semi-automated data acquisition using FEI electron microscope. It features a simple to use interface with easy setup and minimum calibration. The program was tailored to FEI microscope with Gatan K2 Summit camera, but also works with other direct electron detection cameras.

Cite publication: Xueming Li, Shawn Zheng, David A. Agard and Yifan Cheng (2015) Aysnchronous data acquisition and on-the-fly analysis of dose fractionated cryo-EM images by UCSFImage. Journal of Structural Biology, 2015 Nov;192(2):174-8. doi: 10.1016/j.jsb.2015.09.003. Epub 2015 Sep 11. PMID: 26370395


MotionCorr

This program corrects whole frame image motion recorded with dose fractionated image stack.

Cite publication: Xueming Li, Paul Mooney, Shawn Zheng, Chris Booth, Michael B. Braunfeld, Sander Gubbens, David A. Agard and Yifan Cheng (2013) Electron counting and beam-induced motion correction enables near atomic resolution single particle cryoEM. Nature Methods, 10, 584-590. PMID: 23644547


GeFREALIGN

FREALIGN is a program developed by Niko Grigorieff laboratory for high-resolution refinement of 3D reconstruction from cryoEM of single particles. We have modified the original FREALIGN (version v8.06) to run on GPU processors so that the refinement process of single particle 3D reconstruction can be speedup. All the algorithms from the original FREALIGN are kept unchanged.

Cite publication: Xueming Li, Nikolaus Grigorieff and Yifan Cheng (2010) GPU-enabled FREALIGN: Accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors. Journal of Structural Biology, advanced publication online June 14 2010. PMID: 20558298


UCSF Tomography

UCSF Tomography is used to collect single-axis tilt series on electron transmission microscopes. This software was implemented based upon a novel approach in which the Compustage tilting is modeled as geometric rotation. The spatial movement of the sample as a result of stage tilting can be predicted based upon previously collected tomographic images. Therefore, there is no need to collect tracking and focusing images during the entire data collection. A significant dose saving can thus be achieved and is critical in collecting cryo tilt series. This software has been proven to be very robust in collecting cryo tilt series on thin and thick samples at various magnifications up to 60,000x.

Cite publication: Shawn Q. Zheng, Michael B. Braunfeld, John W. Sedat, David A Agard (2004) An improved strategy for electron microscopic tomography J. Struct. Biol. Aug;147(2):91-101.