IMOD

About

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:

• IMOD Plugins

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.

• IMOD - segmenting tubes - a special guide for segmenting "tubes"
• IMOD - stereology plugin - how to use stereology in IMOD

• IMOD - compiling - instructions on compiling the IMOD source code and adding your own plugins.
• Notes on a few of the many IMOD command line programs:
  • IMOD - edmont - gives an example of how to use "edmont" - to help align a montage.
  • IMOD - mtk - an example of how to use "mtk" to find closest distances between surfaces.

Links

• IMOD main site
• IMOD's YouTube channel - created 2012
• IMOD site source doc
• FTP site for latest code / beta version of IMOD - ftp://bio3d.colorado.edu/latestIMOD/
• HTTP version of above - http://bio3d.colorado.edu/ftp
• Plugin instructions - video tutorial I've made for DrawingTools, Interpolator and BeadHelper

Acknowledgements: Brad Marsh and David Mastronarde for introducing me to IMOD and encouraging me to add to its development