IMOD (software)

IMOD

IMOD's 3dmod GUI showing a separating cell.
Developer(s) David Mastronarde et al. at the Boulder Laboratory for 3-D Electron Microscopy of Cells
Stable release
4.3.7 / February 23, 2012
Operating system Windows, Mac OS X, Linux
Type Electron microscopy
License free and opensource
Website bio3d.colorado.edu/imod

IMOD is an open-source, cross-platform suite of modeling, display and image processing programs used for 3D reconstruction and modeling of microscopy images with a special emphasis on electron microscopy data. IMOD has been used across a range of scales from macromolecule structures [1] to organelles [2][3][4] to whole cells [5] and can also be used for optical sections.[6][7] Included in IMOD are tools for image reconstruction, image segmentation, 3D mesh modeling and analysis of 2D and 3D data.

IMOD was developed at the Boulder Laboratory for 3-D Electron Microscopy of Cells. IMOD was first released in 1995,[8] is free to download and use for any purpose.


Main Programs

IMOD includes over 180 command line programs listed here and three main GUI programs:

Supported File Formats

Image Format: The main image format supported by IMOD is MRC file format, which typically have a ".st", ".mrc" or ".rec" extensions and represent various types of "image stacks" which together might represent a tilt series or 3D volume. IMOD will also open TIF files and includes a set of programs to convert between image formats including common microscopy formats like ".raw" and ".dm4". Vector Format: IMOD saves and opens vector data in the form of contour (polygons) and meshes in an IMOD binary file format, typically with a ".mod" or ".fid" extension. These IMOD model files are typically over-laid over the top of an image file and can be used to annotate and segment regions of interest. Models can consists of one or more objects, where each object can contain closed, open or scattered point "contours" which are used to generate a 3D mesh.

Main Features

See also

Wikimedia Commons has media related to IMOD (software).

References

  1. Nicastro, Daniela; Schwartz, Cindi; Pierson, Jason; Gaudette, Richard; Porter, Mary E.; McIntosh, J. Richard (2006). "The Molecular Architecture of Axonemes Revealed by Cryoelectron Tomography". Science. 313 (5789): 944–948. doi:10.1126/science.1128618.
  2. Pelletier, Laurence; O'Tool, Eileen; Schwager, Anne; Hyman, Anthony A.; Müller-Reichert, Thomas (2006). "Centriole assembly in Caenorhabditis elegans". Nature. 444: 619–623. doi:10.1038/nature05318.
  3. Marsh, Brad J.; Mastronarde, David N.; Buttle, Karolyn F.; Howell, Kathryn E.; McIntosh, J. Richard (2001). "Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT-T15, visualized by high resolution electron tomography". Proceedings of the National Academy of Sciences. 98 (5): 2399–2406. doi:10.1073/pnas.051631998.
  4. Hayashi, Mitsuko; Andrea, Raimondi; O'Toole, Eileen; Summer, Paradise; Chiara, Collesi; Ottavio, Cremona; Shawn M., Ferguson; De Camilli, Pietro (2008). "Cell- and stimulus-dependent heterogeneity of synaptic vesicle endocytic recycling mechanisms revealed by studies of dynamin 1-null neurons". PNAS. 105 (6): 2175–2180. doi:10.1073/pnas.0712171105.
  5. Höög, Johanna L.; Schwartz, Cindi; Noon, Angela T.; O'Toole, Eileen T.; Mastronarde, David N.; McIntosh, J. Richard; Antony, Claude (2007). "Organization of Interphase Microtubules in Fission Yeast Analyzed by Electron Tomography". Developmental Cell. 12 (3): 349–361. doi:10.1016/j.devcel.2007.01.020.
  6. Haber, SN; Kim KS; Mailly P; Calzavara R (2006). "Reward-related cortical inputs define a large striatal region in primates that interface with associative cortical connections, providing a substrate for incentive-based learning". J Neurosci. 26 (32): 8368–8376. doi:10.1523/JNEUROSCI.0271-06.2006. PMID 16899732.
  7. Mailly, P; Haber SN; Groenewegen HJ; Deniau JM (2010). "A 3D multi-modal and multi-dimensional digital brain model as a framework for data sharing". J Neurosci Methods. 194 (1): 56–63. doi:10.1016/j.jneumeth.2009.12.014. PMID 20043949.
  8. Kremer, James R.; Kisielowski, David N.; McIntosh, J. Richard (1996). "Computer Visualization of Three-Dimensional Image Data Using IMOD". Journal of Structural Biology. 116 (1): 71–76. doi:10.1006/jsbi.1996.0013.
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