MotionCorr protocols

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MotionCorr specifications


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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  • person_outline Yifan Cheng <>

Publication for MotionCorr

MotionCorr in pipelines

PMCID: 5798934
PMID: 29345620
DOI: 10.7554/eLife.31662.031

[…] of 6803 images, each of which was from a total exposure of 2 s dose-fractionated into seven chunks, were collected at a range of underfocus between 0.5 ~ 3 μm. images were motion corrected using motioncorr (), and the program ctffind3 () was used for determining the defocus and astigmatism. images with poor ctf estimation as well as defocus >3 μm were discarded. the spider software […]

PMCID: 5914886
PMID: 29278985
DOI: 10.1080/15384101.2017.1415680

[…] each were collected at a dose rate of 8 e− per pixel per s, with a total dose of 28 e−/å2., micrographs were processed as previously described [,,]. briefly, frame alignments were performed using motioncorr [], and ctf estimation using ctffind4 []. mts were manually identified and extracted using overlapping square boxes with an edge length of ∼675 å that were spaced ∼80 å apart, […]

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 [] and ctf models were calculated using ctffind3 []. the resulting motion-corrected and signal-integrated micrographs were subjected to automated difference-of-gaussian particle selection […]

PMCID: 5428714
PMID: 28373698
DOI: 10.1038/s41598-017-00533-w

[…] on a 17 hz fei falcon ii direct electron detector. each exposure movie had a total exposure of one seconds and contained seven images., drift-corrected averages of each movie were created using motioncorr and the contrast transfer function of each determined using ctffind3 any images showing signs of significant astigmatism were discarded. all subsequent image processing steps […]

PMCID: 5584162
PMID: 28652389
DOI: 10.1083/jcb.201612195

[…] magnification of 80,000, giving a final size of 1.37 å per pixel., images collected from the titan microscope were processed using the appion pipeline (), including individual frame alignment using motioncorr (), and ctf estimation using ctffind4 (). images from the tecnai f20 microscope were processed using the same software, except for the individual frame alignment. according to a previously […]

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MotionCorr in publications

PMCID: 5945598
PMID: 29749375
DOI: 10.1038/s41467-018-04290-w

[…] . )., a total of 1,111 images were collected in two microscope sessions (414 and 697 micrographs, respectively). image processing was performed with relion 2.0 software,. after motion correction with motioncorr and ctf estimation with gctf, 1,093 images were selected for further image processing. filaments were manually picked with e2helixboxer, after which 245,236 particles were extracted at a bo […]

PMCID: 5902453
PMID: 29662061
DOI: 10.1038/s41467-018-03942-1

[…] with three images per hole, using a gatan k2-summit detector in counting mode and a slit width of 20 ev on a gif-quantum energy filter (supplementary tables , )., as general methodology, motioncorr2 was used for whole-frame motion correction, gctf for estimation of the contrast transfer function parameters, and relion-2.0 for all subsequent steps. local motion was corrected […]

PMCID: 5864754
PMID: 29567962
DOI: 10.1038/s41467-018-03606-0

[…] jianlin lei). for each micrograph stack, 38 frames were collected, with a total electron dose at approximately 60 e-/å2 with an exposure time of 2.25 s. the stacks were first motion corrected with motioncorr and the output stacks were further motion corrected with motioncor2. dose weighting was performed concurrently. gctf was used to estimate the defocus values., a representative diagram […]

PMCID: 5807055
PMID: 29307484
DOI: 10.1016/j.str.2017.12.005

[…] 0-2.5 μm using fei epu software for automated data-collection. a total of 1,405 “movie” mode image stacks were obtained. these image stacks were corrected for the effects of beam-induced motion using motioncorr (). motion-corrected sum images were produced using all recorded frames. image contrast transfer function (ctf) was determined by gctf (), which enabled the selection of 1,280 out of 1,405 […]

PMCID: 5799240
PMID: 29403048
DOI: 10.1038/s41598-017-18962-y

[…] dose of 38 e−/å2 on the specimen. all of the imaging conditions are listed in table ., image processing and 3d reconstruction processes are listed in table . motion corrections were performed with motioncorr before further image processing. ctf parameters of each image were determined with ctffind3. particles were picked automatically with relion1.3, and were further cleaned up through 2d […]

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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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