UCSFImage protocols

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UCSFImage specifications

Information


Unique identifier OMICS_17199
Name UCSFImage
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
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yifan Cheng <>

Publication for UCSFImage

UCSFImage in pipelines

 (2)
2016
PMCID: 5099872
PMID: 27811944
DOI: 10.1038/cr.2016.123

[…] values varied from 1.5 to 2.5 μm. each image was dose-fractionated to 32 frames with a dose rate of ∼8.2 counts/sec/physical-pixel (∼4.7 e−/sec/å2), total exposure time of 8 and 0.25 s per frame. ucsfimage4 was used for all data collection (developed by xl)., a total of 1 064 cryo-em micrographs were collected. all images were aligned and summed using whole-image motion correction. […]

2015
PMCID: 4409540
PMID: 25855297
DOI: 10.1038/nature14367

[…] each image was fractionated into 30 subframes, each with an accumulation time of 0.2 s per frame. all dose-fractionated cryo-em images were recorded using a semi-automated acquisition program ucsfimage4 (written by x. li). images were recorded with a defocus in a range from 1.5 to 2.8 µm., samviewer, an interactive image analysis program written in python, was used for all 2d image […]


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UCSFImage in publications

 (9)
PMCID: 5599796
PMID: 28739580
DOI: 10.15252/embj.201796958

[…] in a reconstruction of the pol i pic at 27 å, which served as a starting model for the cryo‐em dataset., for the cryo‐em dataset, the dose‐fractionated movie frames were processed on‐the‐fly using ucsfimage4 to motion‐correct and sum them (li et al, ). the contrast transfer function (ctf) parameters of the micrographs were estimated using ctffind4 (rohou & grigorieff, ). the thon rings […]

PMCID: 5336481
PMID: 28112729
DOI: 10.1038/nsmb.3362

[…] a vitrobot (fei company) at 100% humidity and 8 °c. the grids were imaged using a titan krios microscope operated at 300 kv, and equipped with a k2 summit electron counting camera (gatan company). ucsfimage4 was used for data collection with nominal magnification of 22,500×, corresponding to an image pixel size of 0.66 å under super-resolution counting mode. images were recorded with defocus […]

PMCID: 5663480
PMID: 28933693
DOI: 10.7554/eLife.26856.018

[…] only, (2) dynamin gmppcp, (3) endophilin-dynamin complex gdp crosslinked with glutaraldehyde. electron cryo-micrographs for all samples were collected using standard low-dose procedures through ucsfimage4 or serialem on a tecnai tf30 polara microscope (fei company, hillsboro, usa) operated at 300 kv (). images were collected at a nominal magnification of 31,000 x (endophilin and co-complex […]

PMCID: 5099872
PMID: 27811944
DOI: 10.1038/cr.2016.123

[…] values varied from 1.5 to 2.5 μm. each image was dose-fractionated to 32 frames with a dose rate of ∼8.2 counts/sec/physical-pixel (∼4.7 e−/sec/å2), total exposure time of 8 and 0.25 s per frame. ucsfimage4 was used for all data collection (developed by xl)., a total of 1 064 cryo-em micrographs were collected. all images were aligned and summed using whole-image motion correction. […]

PMCID: 5192968
PMID: 27534377
DOI: 10.1002/pro.3018

[…] postdoctoral fellow in the laboratory of yifan cheng at ucsf, li introduced the general purpose graphic processing unit (gpgpu) into 3d reconstruction and developed the data collection system named ucsfimage. these efforts resulted in the acceleration of single‐particle cryo‐em data processing by more than 10‐fold. his studies on a new generation of detector (i.e., electron counting camera), […]


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UCSFImage 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
UCSFImage funding source(s)
This work is supported in part by HHMI, a NSF grant DBI-0960271, and NIH grants (5R01GM082893, 5R01GM098672, 2P50GM082250, and 1S10OD020054).

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