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Protocols

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

Subtool


  • ETomo

Versioning


No version available

Publication for IMOD

IMOD citations

 (299)
library_books

Small GTPases and BAR domain proteins regulate branched actin polymerisation for clathrin and dynamin independent endocytosis

2018
Nat Commun
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 […]

library_books

Promotion of virus assembly and organization by the measles virus matrix protein

2018
Nat Commun
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 […]

library_books

The Origin, Dynamic Morphology, and PI4P Independent Formation of Encephalomyocarditis Virus Replication Organelles

2018
MBio
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, […]

library_books

Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell

2018
Sci Adv
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 […]

library_books

Conserved in situ arrangement of complex I and III2 in mitochondrial respiratory chain supercomplexes of mammals, yeast, and plants

2018
Proc Natl Acad Sci U S A
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 […]

library_books

Quantifying exosome secretion from single cells reveals a modulatory role for GPCR signaling

2018
PMCID: 5839777
PMID: 29339438
DOI: 10.1083/jcb.201703206

[…] fei). images (1,024 å ∼ 1,024 pixels) were recorded using an f416 cmos 4,000 × 4,000 pixel camera (tvips). tilt series alignments and weighted back-projection reconstructions were performed using etomo (imod) software. 15 nm protein a gold at the surface of the sections was used as fiducial marker. manual contouring of the tomograms was done using imod program., cells were acquired […]


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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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