The IMOD Home Page

The development of IMOD has been supported by grants from the National Center for Research Resources, the National Institute of General Medical Sciences, and the National Institute for Biomedical Imaging and Bioengineering. IMOD and virtually all programs contained within the IMOD package are Copyright (c) 1994-2009 by the Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells and the Regents of the University of Colorado. Other contributors are acknowledged in our Copyright and Credits statement.

IMOD 3.13 contains a variety of functional enhancements plus the usual assortment of bug fixes. The highlights of this version include:

• In eTomo, the tomogram generation panel was split into two, one for making and processing the aligned stack and one for making the tomogram. There are new interfaces for running CTF correction programs and for erasing gold fiducials from the aligned stack.
• Programs have been added for detecting gold particles in 2D images and in tomograms, providing tools for erasing nearly all the gold in a tilt series.
• An isosurface rendering of image data can now be displayed in the 3dmod model view window.
• A window was added to 3dmod for displaying successive slices in an array of panels.
• Scale bars have been added to 3dmod.
• 3dmod has two plugins contributed by Andrew Noske, one with a set of drawing tools and one to help with fixing large fiducial models.
• There are new clickable installation packages for installing or upgrading IMOD in Windows, and a new package to make it easier to install Cygwin.

Changes in previous versions:

• IMOD 3.11.5.
• IMOD 3.11.2
• IMOD 3.9.3.
• IMOD 3.9.
• IMOD 3.7.7.
• IMOD 3.7.3.
• IMOD 3.5.5.
• IMOD 3.5.3
• IMOD 3.3.10.
• IMOD 3.3.7.

OpenGL: IMOD requires OpenGL libraries.

Java for eTomo: The eTomo program for building tomograms requires a Java run-time environment. We provide links to Java packages for Linux, Windows, and SGIs on the Download page. Java is part of the standard installation of Mac OS X and comes in some Windows installations too. The Java version that comes in Fedora Core does not work for eTomo.

Cygwin for Windows: For full functionality, the Windows version requires installation of a Unix toolkit called Cygwin. We provide a package for installing this on the Download page.

The recommended configuration for running the IMOD software on a Linux PC is:

• Processor: Any modern Intel or AMD processor.
• Video Cards: Any relatively modern Nvidia-based card (128 MB or higher cards preferred)
• Minimum recommended memory size: 512MB
• Minimum recommended disk size: 30 GB
• Operating System: Red Hat Workstation 4 or Fedora 4 installation or higher
• Nvidia Linux device drivers, version 1.0-8776 or later, and OpenGL libraries from Nvidia

Notes and caveats on Linux systems:

• Use a video card other than Nvidia at your own risk. We have limited experience with ATI cards; an ATI 9800SE appeared to work fine but several serious problems have occurred with Fire GL cards. Having a top-of-the-line Nvidia card is not essential. Historically, 3dmod's graphics performance depended heavily on processor speed and memory bandwidth and not much on the grade of the card; but we have recently seen Quadro cards having advantages. The performance dropped about 50% after the 100.14.19 drivers and has not improved since (as of the 180.29 drivers).
• More memory is generally better, since 3dmod works best when it can load all of an image file in memory (one byte per pixel). For generating and studying tomographic reconstructions, 4 GB is recommended.
• We generally work on, and thus can directly support, only one or two versions of Linux. Currently we are working under Red Hat Enterprise Linux 5 but still run Fedora Core 2 and 4 for builds.

Performance notes:

• Computational performance on PowerPC-based Macs (G4, G5) has generally been disappointing, while performance on Intel-based Macs is mostly comparable to that in Windows and Linux. The version for Intel Macs does almost as well as the 64-bit Linux version with an equivalent processor even though it is still only 32-bit.
• The version for 64-bit Windows is nearly a factor of two faster than the 32-bit version for some tasks, such as tomogram generation with local alignments, and combining dual-axis tomograms.

• The IMOD User's Guide with installation and other general information.
• The Introduction to 3dmod, which provides a comprehensive tour of the major features of the 3dmod image display and modeling program.
• A Tomography Guide, with detailed instructions on building tomograms with the IMOD package, as well as a guide to joining tomograms from serial sections.
• A Tutorial for building a dual-axis tomogram with eTomo, and a sample data set.
• A Tutorial for joining serial section tomograms with eTomo, and a sample data set.
• The current listing of all programs in the IMOD software package, with links to manual pages.
• Documentation of IMOD C library functions, including instructions on building a plugin for 3dmod.
• The original publication describing an early version of the IMOD software is Kremer J.R., D.N. Mastronarde and J.R. McIntosh (1996) Computer visualization of three-dimensional image data using IMOD J. Struct. Biol. 116:71-76. For tomographic reconstruction, see Mastronarde, D.N. (1997) Dual-axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 120:343-352.
• Example images of IMOD model renderings.
• Instructions for joining the IMOD Discussion List.
• Sample data files that can be used to experiment with IMOD are available in a gzipped tar archive: imod_data.tar.gz
• Source code is available in complete form for approved non-profit organizations only, but an open-source subset is also available.