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Unblur specifications

Information


Unique identifier OMICS_26911
Name Unblur
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format MRC/CCP4
Operating system Unix/Linux
Computer skills Advanced
Version 1.0.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Nikolaus Grigorieff <>

Publication for Unblur

Unblur in pipelines

 (10)
2018
PMCID: 5758107
PMID: 29249608
DOI: 10.1016/j.str.2017.11.011

[…] 2 s exposure/frame) in counting mode were collected per tilt at a dose rate of ∼5e-/unbinned pix/sec, giving an overall dose of ∼ 60 e-/å2. frames were aligned and filtered for radiation damage using unblur (). tomograms were reconstructed using imod (). contrast transfer functions were measured and data phase-flipped in imod. tomograms were further processed for viewing in fiji (). subvolumes wer […]

2018
PMCID: 5807054
PMID: 29395787
DOI: 10.1016/j.str.2017.12.014

[…] every four frames were binned together. the defocus range was 1.3-3.1 μm in 0.3 μm increments; defocus was measured in the autofocus routine every 10 μm., whole-frame alignment was performing using unblur () before ctf estimation using ctffind4 (). all resolution estimates are based on the fsc = 0.143 criterion, and the final resolution estimates were made after the application of a binary mask […]

2018
PMCID: 5889399
PMID: 29626188
DOI: 10.1038/s41467-018-03677-z

[…] pixel size of 1.4 å per pixel on the object scale. data were collected in a defocus range of 10 000–30 000 å with a total exposure of 100 e å−2. forty frames were collected and aligned with the unblur software package using a dose filter., several thousand particles were manually picked and carefully cleaned in xmipp to remove inconsistent particles. the resulting useful particles were used […]

2018
PMCID: 5935684
PMID: 29728587
DOI: 10.1038/s41598-018-25429-1

[…] an image pixel size of 1.4 å per pixel on the object scale. data were collected in a defocus range of 10 000–40 000 å with a total exposure of 100 e/å2. 40 frames were collected and aligned with the unblur software package with a dose filter. we collected ~2000 micrographs from several independent ncp preparations. several thousand particles were manually picked and carefully cleaned in xmipp […]

2017
PMCID: 5344670
PMID: 28092267
DOI: 10.7554/eLife.24149.020

[…] in total, 4339 movies were recorded, from which ~35,000 particles were used in final reconstructions ( and )., the raw frame stacks were gain-normalized and then aligned and dose-compensated using unblur () (). ctf was estimated from the aligned frame sums using ctffind4 (). to reduce the possibility of bias and capture every possible particle view, an initial set of 350,000 potential […]


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Unblur in publications

 (35)
PMCID: 5908803
PMID: 29674684
DOI: 10.1038/s41467-018-03881-x

[…] of ×75,000 (yielding a pixel size of 1.10 å), with a dose rate of approximately 0.8 e− å−2 s−1, and a defocus range between 1.0 and 3.5 μm. exposure of 50 s yielded 50 frames in total., we use unblur for whole-frame motion correction and exposure weighting, gctf for estimation of global and local contrast transfer function (ctf) parameters, gautomatch (developed by zhang k, mrc laboratory […]

PMCID: 5862660
PMID: 29413413
DOI: 10.1016/j.ultramic.2018.01.011

[…] 1fig. 1fig. 2fig. 2, to calculate quantitatively the image contrast and allow it to be plotted as a function of defocus, as shown in , the frames of each movie were first aligned using the program unblur . each image was then examined to find bright diffraction beams from gold nanoparticles that were oriented in diffracting positions, as seen with the boxed particle in (a) that has two […]

PMCID: 5816019
PMID: 29453354
DOI: 10.1038/s41467-018-03164-5

[…] (0.3 s/frame) and a total exposure of ~40 e/å2., the movie frames collected on the k2 summit were background corrected before motion correction was applied by aligning the frames with the program unblur. all frames were used in the final frame sums. furthermore, the images collected on the titan krios were corrected for magnification distortion using the program mag_distortion_correct. fibril […]

PMCID: 5807054
PMID: 29395787
DOI: 10.1016/j.str.2017.12.014

[…] every four frames were binned together. the defocus range was 1.3-3.1 μm in 0.3 μm increments; defocus was measured in the autofocus routine every 10 μm., whole-frame alignment was performing using unblur () before ctf estimation using ctffind4 (). all resolution estimates are based on the fsc = 0.143 criterion, and the final resolution estimates were made after the application of a binary mask […]

PMCID: 5758107
PMID: 29249608
DOI: 10.1016/j.str.2017.11.011

[…] 2 s exposure/frame) in counting mode were collected per tilt at a dose rate of ∼5e-/unbinned pix/sec, giving an overall dose of ∼ 60 e-/å2. frames were aligned and filtered for radiation damage using unblur (). tomograms were reconstructed using imod (). contrast transfer functions were measured and data phase-flipped in imod. tomograms were further processed for viewing in fiji (). subvolumes wer […]


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Unblur institution(s)
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA

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