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) 1994-2011 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 4.5 contains several major functional enhancements plus the usual assortment of bug fixes. The highlights of this version include:

• The PEET interface in eTomo is upgraded and clarified and has changes to work with PEET version 1.8.
• The 3dmod Model View window uses buffers that can be stored on the graphics card, speeding up display of meshed surfaces by up to 40 times (depending on the number of cores in the graphics card). Sphere and line drawing are also somewhat faster.
• There are new programs for pasting multiple, rotated copies of a model or subvolume into a larger model or image volume, respectively.
• Dependence of C-shell scripts is virtually eliminated and thus this version can be run with current versions of Cygwin on Windows.

IMOD 4.5.7 is an update with some minor bug fixes, listed here. Here is the complete list of changes in the first release of IMOD 4.5.

Changes in previous versions:

• IMOD 4.3.7
• IMOD 4.3
• IMOD 4.1.10
• IMOD 4.1
• IMOD 3.13.6.
• IMOD 3.13
• IMOD 3.11.5.
• IMOD 3.11.2
• IMOD 3.9.3.
• IMOD 3.9.

Java for eTomo: The eTomo program for building tomograms requires a Java run-time environment. We provide links to Java packages for Linux and Windows on the Download page. However, Java comes in many Windows installations, and the Java versions that come in current Fedora Core, Red Hat Enterprise, and Ubuntu distributions also usually work with eTomo (see the IMOD Guide for details).

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. IMOD 4.5 should also run reliably on more current versions of Cygwin, even on 64-bit Windows.

OpenGL: IMOD requires OpenGL libraries.

The recommended configuration for running the IMOD software is:

• Processor: Any modern Intel or AMD processor.
• Video Cards: Any relatively modern Nvidia-based card (256 MB or higher cards preferred); ATI cards also work on Windows and Mac.
• Minimum recommended memory size: 1 GB (Linux and Mac) or 2 GB (Windows)
• Minimum recommended disk size: 60 GB
• Operating System: Linux - Red Hat Workstation 5 or 6 or Fedora 6 installation or higher (or equivalent level for Ubuntu or Suse). Windows - Windows XP, Vista, or Win 7. Mac - OS X 10.5 or higher (The PowerPC 32-bit package will still work under OS X 10.4).
• On Linux, Nvidia device drivers and OpenGL libraries from Nvidia

Notes:

• Graphics Performance. Starting with IMOD 4.5, graphics performance for viewing models depends strongly on the number of cores in the graphics card GPU, but getting a top-of-the-line card is not essential unless you will be working with exceptionally large models. Quadro cards may have better performance per core than GeForce cards, but the price/performance ratio is much poorer.
• ATI versus Nvidia. With Linux, ATI cards have historically been problematic for OpenGL in IMOD. More recently, users report mostly good results but still some problems with ATI cards in laptops. We are not currently able to address problems with ATI cards in Linux. The situation is better with Windows and Mac OS X, where the ATI drivers have been more reliable. We do have a 64-bit Windows system where we can examine ATI graphics problems.
• Linux Versions Supported. 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 6 but still run older Red Hat and Fedora for builds, have access to a recent Fedora version, and can boot an Ubuntu system when necessary.
• Memory. 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, at least 8 GB is recommended.

• 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. This is a binned down data set that matches what is used in the tutorial document.
• Tutorial videos on YouTube. Here is the unbinned data set that matches what is used in the videos. It is 200 MB. You can use this for working through the tutorial document, but various things will not match the screen shots there. Unpack this file with the command:
      tar -xzf tutorialData-1K.tar.gz
• 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 and signing up on a separate mailing 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 also available.
• Matlab code for accessing IMOD models and MRC image files is available in the PEET package.