MotionCorr pipeline

MotionCorr specifications

Information


Unique identifier OMICS_17200
Name MotionCorr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yifan Cheng <>

Publication for MotionCorr

MotionCorr IN pipelines

 (6)
2018
PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986

[…] micrographs were collected in ~72 h. the total dose received for each movie micrograph was 67 e-/å2. the nominal defocus range used was -1.5 to -4.0 μm., movie micrograph frames were aligned using motioncorr [57] and ctf models were calculated using ctffind3 [58]. the resulting motion-corrected and signal-integrated micrographs were subjected to automated difference-of-gaussian particle […]

2016
PMCID: 4762201
PMID: 26829225
DOI: 10.1038/nature16940

[…] we used a slit width of 20 ev on a gif quantum energy filter. each image was exposed for a total of 16 seconds and dose-fractionated into 20 movie frames. a defocus range of 0.5-3.5 μm was used., motioncorr51 was used for whole-image drift correction of the movie frames of each micrograph, and contrast transfer function (ctf) parameters of the corrected micrographs were estimated using […]

2016
PMCID: 4823867
PMID: 27048994
DOI: 10.1038/ncomms11293

[…] 47 e− per å2 fractionated over 20 frames with a calibrated pixel size of 0.715 å for the super-resolution micrographs., micrograph frame stacks were binned by two, subjected to drift-correction using motioncorr39 and contrast transfer function (ctf) parameters were determined using gctf40. an initial model for refinement was generated using eman2 (ref. 41). all subsequent image processing steps we […]

2016
PMCID: 5146279
PMID: 27905396
DOI: 10.1038/ncomms13681

[…] the dose fractioned image stacks were binned 2 × 2 by fourier cropping, resulting in 3,838 × 3,710 pixels with a pixel size of 1.232 å. the stacked frames were subjected to motion correction with motioncorr35. ctf determination was performed using ctffind3 (ref. 36). eman2 (ref. 37) was used for particle picking and making the initial three-dimensional model. for the inx-6 hemichannel, 1,053 […]

2016
PMCID: 5156311
PMID: 27459055
DOI: 10.1038/nature19316

[…] and a calibrated pixel size of 1.43 å. a total dose of 40 e å-2 over 16 s and a defocus range of 0.5 – 4 μm were used., a total of 2213 micrographs were subjected to whole-frame drift correction in motioncorr56 followed by contrast transfer function (ctf) parameter estimation in ctffind4 (ref. 57). all subsequent processing steps were done using relion58 unless otherwise stated. an initial […]

MotionCorr institution(s)
The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA; The Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA; Gatan Inc., Pleasanton, CA, USA
MotionCorr funding source(s)
This work is supported by the UCSF Program for Breakthrough Biomedical Research and NIH grants (R01GM082893, R01GM098672 and P50GM082250).

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