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UCSF Tomography specifications


Unique identifier OMICS_17201
Name UCSF Tomography
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes




No version available


  • person_outline David Agard <>

Publication for UCSF Tomography

UCSF Tomography citations


Three dimensional structural dynamics of DNA origami Bennett linkages using individual particle electron tomography

PMCID: 5807444
PMID: 29426880
DOI: 10.1038/s41467-018-03018-0

[…] tf20 tem (five series) and a zeiss libra 120 plus tem (15 series). on the fei tecnai tf20 tem (operated at 200 kv), the tilt series were collected from − 48 ° to + 48 ° at 1.5 ° increment using ucsf tomography software package and a gatan k2 summit direct electron detection camera at ~ 1 μm defocus and a magnification of 19 kx. at this magnification, the pixel size of the micrographs […]


FtsEX mediated regulation of the final stages of cell division reveals morphogenetic plasticity in Caulobacter crescentus

PMCID: 5607218
PMID: 28886022
DOI: 10.1371/journal.pgen.1006999

[…] microscope (fei) equipped with a gif energy filter (gatan) and a k2 summit direct detector (gatan). tilt-series were collected from -50° to +50° in 1° increments at magnification of 22,500x using ucsf tomography software [] with a defocus of -12 μm and total dosage of 180 e-/å2. tomograms were calculated using imod software []., rosetta(de3)plyss e. coli cells containing overexpression […]


Fully Mechanically Controlled Automated Electron Microscopic Tomography

PMCID: 4941525
PMID: 27403922
DOI: 10.1038/srep29231

[…] incorporated into a gatan digital micrograph (dm)-based tomography software, integrating both manual and automated data collection., in our method, compared to other et control software, such as ucsf tomography and serial em (), the major benefits include keeping the pre-aligned/optimized beam conditions unchanged and achieving position tracking solely through mechanical (goniometer) […]


3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

PMCID: 4419541
PMID: 25940394
DOI: 10.1038/srep09803

[…] operation using gatan tomography software (for zeiss libra 120 tem) that had been preinstalled in the microscopes. micrographs were initially aligned together with the imod software package or ucsf tomography. the defocus near the tilt-axis area of each tilt micrograph was examined by fitting contrast transfer function (ctf) parameters with its power spectrum using ctffind3 in the frealign […]


Ring closure activates yeast γTuRC for species specific microtubule nucleation

PMCID: 4318760
PMID: 25599398
DOI: 10.1038/nsmb.2953

[…] a polara electron microscope (fei, inc.) running at 300kv. a post-column energy filter (gif, gatan, inc.) was used and the slit width was set at 25 ev. automatic data collection was carried out by ucsf tomography software . single-axis tilt series were collected at a nominal magnification of 41,000. images of dimension 2032x2032 were recorded on a ccd camera (ultracam, gatan, inc.). the final […]


Correlated cryogenic photoactivated localization microscopy and electron cryotomography

PMCID: 4081473
PMID: 24813625
DOI: 10.1038/nmeth.2961

[…] the finder-grid were used to locate the cells imaged by cryo-palm. energy-filtered tilt-series of images on individual cells were collected automatically from −60° to +60° at 1° intervals using the ucsf tomography data collection software with total dosage of 180 e−/å2 and a defocus of −10 µm. three-dimensional reconstructions and segmentations were produced with imod., to overlay the cryo-palm […]

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UCSF Tomography institution(s)
The Howard Hughes Medical Institute, University of California, San Francisco, CA, USA; The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
UCSF Tomography funding source(s)
This work was supported by funds from the Howard Hughes Medical Institute and the W.M. Keck Advanced Microscopy Laboratory at UCSF.

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