RAPTOR specifications

Information


Unique identifier OMICS_15668
Name RAPTOR
Alternative name Robust Alignment and Projection Estimation for Tomographic Reconstruction
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Mark Horowitz <>

Publication for Robust Alignment and Projection Estimation for Tomographic Reconstruction

RAPTOR in publications

 (7)
PMCID: 5758724
PMID: 29311627
DOI: 10.1038/s41598-017-18115-1

[…] data-collection software,. images were collected at a nominal magnification of 25,000x to a final pixel size of 0.81 nm from a cumulative dose of ∼ 120e−/å2., tomograms were reconstructed using raptor and the imod package (imod v4.8.41, peet v1.10.1, etomo v4.8.41). flagellar motors were manually picked and aligned from tomograms using peet. fsc curves were determined from the final […]

PMCID: 3847603
PMID: 24292151
DOI: 10.1038/ncomms3856

[…] was 180-220 e−/å2. ucsf tomo was used for automatic acquisition of tilt-series and 2d projection images. three-dimensional reconstructions were calculated using the imod software package or raptor. tomograms were visualized using 3dmod. density profiles were generated using imagej., newly synthesized peptidoglycan was labeled using fluorescent d-amino acids. a. castellanii cells […]

PMCID: 3778437
PMID: 24062940
DOI: 10.7554/eLife.00951.018

[…] of 19,500×, giving a pixel size of 4.3 å at the specimen level., tomograms were aligned based on the positions of gold fiducials and reconstructed by weighted back-projection, using the imod () and raptor () software packages. visual analysis and segmentation of reconstructed tomograms were performed with amira (visualisation sciences group, an fei company) and chimera (). sub-tomogram […]

PMCID: 3304575
PMID: 22158337
DOI: 10.3791/2770

[…] number of positions are designated. define batch parameters (±60° with 2° tilt increments, 1-2 e-/å2/tilt view) and run the batch., align tilt series using automatic fiducial-based alignment in raptor 1., reconstruct tomograms using r-weighted back projection in imod 8. the standard file format for the resulting data volumes is the mrc file, with file extension .mrc., this section uses […]

PMCID: 2957311
PMID: 20944740
DOI: 10.1038/nature09423

[…] at: http://bio3d.colorado.edu) adapted for operating jeol microscopes. raw tomographic image stacks were aligned either manually with the etomo suite of progams, or automatically using the software raptor. tomographic reconstructions were constructed using the etomo suite of programs and visualized using the imod software package., the tomograms displayed in were derived from tilt series […]


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RAPTOR institution(s)
Department of Electrical Engineering, Stanford University, Stanford, CA, USA; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
RAPTOR funding source(s)
This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

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