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IMOD specifications

Information


Unique identifier OMICS_27358
Name IMOD
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 4.9.6
Stability Stable
Maintained Yes

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Publication for IMOD

IMOD in pipelines

 (33)
2018
PMCID: 5758107
PMID: 29249608
DOI: 10.1016/j.str.2017.11.011

[…] 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 were picked manually in imod and subvolume […]

2017
PMCID: 5345008
PMID: 28281671
DOI: 10.1038/srep44176

[…] tilt series was kept under 80 electrons/å2 to minimize radiation damage. the tilt series were aligned using gold fiducials, and tomograms were reconstructed using filtered back projection or sirt in imod, as previously described., in this phage adsorption study, 178 subtomograms of infecting phages attached to or near the cell surface were extracted from 16 tomograms of phage-infected cells. […]

2017
PMCID: 5376648
PMID: 28332496
DOI: 10.1038/ncomms14813

[…] 0.35 nm final pixel size, −2,5 μm defocus) with the fei tomography software 4.0., all tomograms were aligned using the 10 nm fiducial gold beads and reconstructed by r-weighted back projection with imod. note that we carefully analysed the tomograms to ensure that the vitreous ice was thicker than the cartwheel lattice to prevent artefacts of the air–water interface., for subtomogram averaging, […]

2017
PMCID: 5437026
PMID: 28522842
DOI: 10.1038/s41598-017-02292-0

[…] of our final dataset using a gaussian sphere as a starting model, yielding essentially identical results (supplemental fig. )., the calculated 3d reconstruction was visualized in ucsf chimera and imod, . the map has been deposited in the electron microscopy data bank, with accession number emd-3655., , electronic supplementary material , supplementary information accompanies this paper […]

2017
PMCID: 5655137
PMID: 29027901
DOI: 10.7554/eLife.28560.031

[…] step was done with three-dimensional (3d) masks that included rnap with or without s1. in both cases, the resulting 30s•rnap classes contained prominent s1 density. the 3d masks were created using imod and eman2 () by generating a density map, low-pass filtered to 20 å, from our initial atomic models of rnap with or without s1 (rnap mask was used for 30sδs1•rnap data). the mask was applied […]


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IMOD in publications

 (288)
PMCID: 5943408
PMID: 29743604
DOI: 10.1038/s41467-018-03955-w

[…] control and image acquisition was accomplished using the software serialem. tilt series were later reconstructed using weighted back projection and fiducial markers (10 nm) into a single volume with imod. to examine areas with the greatest electron density in an unbiased manner, density-based thresholding was employed with the isosurface render programme in imod as previously described […]

PMCID: 5928126
PMID: 29712906
DOI: 10.1038/s41467-018-04058-2

[…] scripts (de_process_frames-2.8.1.py and de_damage_compensate-1.0.0.py) provided by direct electron. tomograms were reconstructed from the aligned images and ctf corrected by phase flipping using the imod software package, . 3d volumes were segmented manually using the amira software program (fei visualization sciences group, hillsboro, or)., linear density profiles were measured […]

PMCID: 5904412
PMID: 29666283
DOI: 10.1128/mBio.00420-18

[…] automated tilt series acquisition was performed using xplore3d software (thermo fisher scientific). tilt series alignment and tomogram reconstruction by weighted back-projection were carried out in imod () (version 4.7.15). in the process, the gold fiducial markers were digitally erased to be eliminated from the final 3d reconstruction. to determine the sizes of ros spanning multiple sections, […]

PMCID: 5930395
PMID: 29725615
DOI: 10.1126/sciadv.aar3219

[…] and high tilts on the 80-nm-thick sections). the resulting images had pixel sizes of 0.19 nm. the images from the tilt series were aligned, filtered, and reconstructed into a tomogram using the imod software package (). the movies for the raw tilt series and reconstruction were carried out using imod, whereas the movies with 3d volume with solid and surface rendering were generated using […]

PMCID: 5866595
PMID: 29519876
DOI: 10.1073/pnas.1720702115

[…] below 80 e−/å2. all tilt series were collected at 4- to 6-µm defocus with the automatic data collection program latitude (gatan)., tilt series were aligned and tomograms were reconstructed using imod (). contrast was enhanced by nonlinear anisotropic diffusion (). subvolumes containing complex i were extracted from the unfiltered tomogram and aligned in peet () using predefined angles […]


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IMOD institution(s)
Boulder Laboratory for 3D Electron Microscopy of Cells, Department of MCD Biology, University of Colorado, Boulder, CO, USA
IMOD funding source(s)
Supported by Grant RR00592 from the National Institutes of Health.

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