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) 1994-2008 by the Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells and the Regents of the University of Colorado.

IMOD 3.11 contains some major functional enhancements plus the usual assortment of bug fixes. The highlights of this version include:

• eTomo has new interfaces for refining the alignment with a model after joining serial sections, for running our 3D particle averaging software, PEET, and for filtering by anisotropic diffusion.
• The 3dmod Slicer window has been changed to work better, more intuitively and like other windows; e.g., the image pans with the mouse. A new dialog has been added to allow slicer angles and positions to be saved and restored.
• Other changes to 3dmod include an upgrade to the XYZ window to add a toolbar and make it easier to use when zoomed up, and a new Locator window allowing one to see and change the location displayed in the Zap window.
• An iterative reconstruction technique, SIRT, is now available and will work with local alignments.
• Programs have been added for measuring defocus in a tilt series and correcting for the microscope CTF.
• Programs have been added for stitching together laterally adjacent tomograms.
• Parallel processing can now be done by submitting to a cluster queue.
• Non-perpendicularity of beam and tilt axis can now be solved for and corrected for.
• The program for cutting out image areas inside model contours has been upgraded and enhanced.

Changes in previous versions:

• 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.
• IMOD 3.1.6

OpenGL: IMOD requires OpenGL libraries. Hardware accelerated 24-bit graphics is recommended for viewing models.

Qt: IMOD requires Qt libraries. Qt is a graphical interface toolkit and is not related to Quicktime. The IMOD package for Fedora Core 4 runs with the default installed Qt library, while the packages for Red Hat 9.0 and Fedora Core 2 include a Qt library so that this package will be forward-compatible to other systems. The packages for Mac, Windows, and SGI include the Qt library. Older versions of IMOD (2.xx) require Motif libraries instead.

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 or Fedora 2 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.
• 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, 2-4 GB is recommended.
• For tomography, the equivalent of a Pentium 4 processor faster than 2.5 GHz and at least 120 GB of disk space is recommended. Slower speeds are equivalent to this for some of the newer architectures (e.g., Opteron, Core Duo). A 7200 RPM SATA drive is adequate.
• We generally work on, and thus can directly support, only one or two versions of Linux. Currently we are working under Fedora Core 4 but still run Red Hat 9.0 and Fedora Core 2 for builds.

Performance notes:

• With the 64-bit version for AMD Opteron or AMD64, we have seen nearly a factor of 2 speed improvement over Pentium 4 for a number of operations, including tomogram generation with local alignments, and combining dual-axis tomograms. Intel Pentium 4-based EM64T processors showed improvements that were similar but not as big. The new dual core Xeon 51xx processors are about 25% faster than equivalent Opterons.
• 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 Linux version with a 51xx processor even though it is still only 32-bit.
• Computational performance under 32-bit Windows is actually a bit better than under 32-bit Linux because programs were compiled with Intel rather than Gnu compilers. Graphics performance is comparable.
• The version for 64-bit Windows has shown most of the advantages for 64-bit versions that are described above for Linux.

• 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.