Summovie protocols

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Summovie specifications

Information


Unique identifier OMICS_26912
Name Summovie
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0.2
Stability Stable
Maintained Yes

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  • person_outline Nikolaus Grigorieff <>

Summovie in pipeline

2016
PMCID: 5041491
PMID: 27563056
DOI: 10.1093/nar/gkw708

[…] images, such as images recorded out of focus, were removed by manual inspection. pixel outliers were removed using the clip function in imod ()., frames were aligned and integrated using the unblur-summovie software () without applying dose weighting. particles were picked semi-automatically in eman2 () and then extracted and processed in relion 1.3 (). the particles were sorted by 2d and 3d […]


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Summovie in publications

 (4)
PMCID: 5607996
PMID: 28570515
DOI: 10.3791/55448

[…] path pattern " by selecting a raw unaligned movie micrograph and replacing the variable part of the file names with the wildcard "*" (e.g., tcda1_*.mrc). specify the path for "output directory".set "summovie executable path" by selecting the executable file.set "number of movie frames" to the number of frames in each movie micrograph. set the "microscope voltage" and "per frame exposure" […]

PMCID: 5472438
PMID: 28548638
DOI: 10.7554/eLife.27389.032

[…] of 2.92 electrons⋅pixel−1⋅subframe−1. after binning by two and motion correction, each image was 4k ×4k and 1.35 å per pixel., the dataset was motion corrected and dose weighted using unblur and summovie (; ; ). motion-corrected micrographs without dose weighting were used for contrast transfer function (ctf) estimations. motion-corrected micrographs with dose weighting were used […]

PMCID: 5745081
PMID: 29280731
DOI: 10.7554/eLife.30483.037

[…] each movie was performed using motioncorr (). a second round of whole-image drift correction was performed using unblur () and the aligned movies were summed and exposure-filtered using the program summovie (). the ctf was determined using ctffind4 () in the relion workflow (). a dataset containing 11,457 particle images manually picked with eman boxer () (324 pixels x 324 pixels) was subjected […]

PMCID: 4848044
PMID: 26789246
DOI: 10.1038/nature16506

[…] using the program unblur,. next, the drift-corrected frames were summed into single micrographs, which were used to estimate the contrast transfer function (ctf) using ctffind4. the program summovie was used to recalculate the summed images, first with a low-pass filter for autopicking and then with the noise power restored after filtering for particle extraction. autopicking, particle […]


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