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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

 (497)
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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
call_split See protocol

[…] 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 for APEX/D […]

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Anatomical Inputs From the Sensory and Value Structures to the Tail of the Rat Striatum

2018
Front Neuroanat
PMCID: 5943565
PMID: 29773980
DOI: 10.3389/fnana.2018.00030
call_split See protocol

[…] acers (Figures , ), the outlines of the cortex, striatum and fluorescent signals of injected retrograde tracers were drawn through 400-μm interval brain slices, and the images were reconstructed with IMOD, a 3D rendering program (Boulder Laboratory, University of Colorado, Boulder, CO, USA). To count the labeled cells, we scanned at 200-μm intervals from three hemispheres (rat #2 right, left and r […]

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

[…] g the EMAN2 command e2proc2d.py input.mrc output_powerspectrum.mrc --process=math.realtofft. Volumes of the F and H layer (~8 nm thickness) were projected onto the XY plane along the Z-axis using the IMOD command xyzproj, separately. The power spectra of the 2D projections were generated using EMAN2 command as described above (Supplementary Figure ). The threshold was adjusted manually to a level […]

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Isolation of mitochondria from Saccharomyces cerevisiae using magnetic bead affinity purification

2018
PLoS One
PMCID: 5919621
PMID: 29698455
DOI: 10.1371/journal.pone.0196632
call_split See protocol

[…] d mitochondria were imaged and included in subsequent analysis, and representative data were collected from both crude and bead-purified mitochondria. Tomograms were aligned using fiducial markers in IMOD version 4.9 [, ], followed by three-dimensional volume reconstruction of 3x-binned tilt series via a simultaneous iterative reconstruction technique (SIRT), using Tomo3D []. Volumes were subseque […]

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, t […]

library_books

Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell

2018
Sci Adv
PMCID: 5930395
PMID: 29725615
DOI: 10.1126/sciadv.aar3219

[…] tilts 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 UCS […]

Citations

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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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