IMOD

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About

Imod 3dmod main interface screenshot.png

IMOD is a free set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of Electron Microscopy (EM) serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed at the Boulder Laboratory for 3-D Electron Microscopy of Cells. The main author and contact person for IMOD is David Mastronarde. David also developed and maintains Serial EM - a electron microscope control program which integrates with IMOD.

IMOD is a program I've relied on heavily for my research - helping me acquire, reconstruct, segment and analyze tomograms - and so I've created several tutorials and instructions wiki pages to give advice help document various IMOD functionality. I've listed all these pages below under "Child Pages".


Imod Plugins

In addition to using IMOD, I've worked a lot with David to develop and add several of my own plugins to IMOD. These plugins include "Drawing Tools", "Interpolator", "BeadHelper" and "Name Wizard", which I've explained in greater detail (and with videos) on this page:


Child Pages

Related/Child Pages:
  • IMOD - tutorial - a few notes I tried to put together from a couple of very small IMOD tutorials I've run.
  • IMOD - segmenting datasets - a quick-start guide for anyone wishing to segment datasets in 3dmod.
  • IMOD - preparing images for publication - (**) useful instructions on how to output high resolution, publication quality images from IMOD.
  • IMOD - making movies - (**) useful instructions on how to generate a movie from 3dmod's ZAP or ModelView window.
  • IMOD - naming objects - explains the importance of and how to use standard names (and colors) to label objects (the best way being "Name Wizard")!
  • IMOD - segmentation standards - expands on the "naming objects" examples and list some of the "standard names and colors tables" I've used.
  • IMOD - file formats - talks about what file formats IMOD accepts and how to convert between several different formats.



Links


Acknowledgements: Brad Marsh and David Mastronarde for introducing me to IMOD and encouraging me to add to it's development