The IMOD Home Page
Boulder Laboratory for 3-D Electron Microscopy of Cells
IMOD is a set of image processing, modeling and display
programs used for tomographic reconstruction and for 3D reconstruction of 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 primarily by David
Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John
Heumann at the Boulder Laboratory for 3-D Electron Microscopy of Cells.
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.
virtually all programs contained within the IMOD package are
Copyright (c) 1994-2014 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 4.7 Is Now Available for Linux, Windows, and Mac OS X
DOWNLOAD IMOD 4.7
Download Alpha or Beta Development Versions (IMOD 4.8.x)
Hardware and Operating System Requirements
IMOD Guides, Assistance and Information
IMOD Discussion and Mailing Lists (subscribing
IMOD Source Code
SerialEM Tilt Series Acquisition Software
IMOD 4.7 contains a variety of major functional enhancements plus the usual
assortment of bug fixes. The highlights of this version include:
- Tomogram Processing
- There is a new program for automatically picking a well-distributed
set of fiducials for a seed model, with an interface in eTomo.
- The bead tracker can now refine center positions using an edge-detecting
filter, which significantly reduces the alignment mean residual for
both plastic and cryo data sets.
- The fine alignment can now be done with robust fitting, which
eliminated or down-weights points with exceptionally high residuals.
- It is now possible to build tomograms automatically with fiducial,
patch tracking, or fiducialless alignment using the script
- Templates can be defined from one data set for setting selected
parameters in other similar data sets; eTomo has an editor for saving
- There is an interface for aligning serial sections or just blending
montages in eTomo; this alignment can be done with 2D warping computed
by cross-correlation of subareas.
- 3dmod can access multiple copies of the same volume at different
resolutions and has a new kind of cache that allows rapid access to
subareas at any zoom.
- The Slicer window was enhanced with arrows for rotating around viewer
axes, a slider for scrolling through slices, and a rubber band for
resizing the window or image or for extracting a rotated file.
- It is possible to model in all three planes of the XYZ window, and
contours drawn in any plane can be meshed easily.
- A new dialog allows saving, running, and modifying a sequence of movie
segments set up in the Model View Movie dialog.
- Jane Ding at Caltech contributed the Grab with Note plugin, which takes
snapshots of the Slicer or Zap window with text annotations and details
about the image.
- Virtually all programs can now read TIFF files and the MRC-like files
read by 3dmod (including DigitalMicrograph).
- It is now possible to install IMOD and use virtually all features on
Windows without installing Cygwin.
Here is the complete list of changes in
IMOD 4.7, and a list of bug fixes in the
latest update, IMOD 4.7.8.
Changes in previous versions:
Hardware and Operating System Requirements
Java for eTomo: The eTomo program for building tomograms requires a
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).
For Mac OS X 10.7 and higher, Java is not available initially but the system
will offer to install it when you run a Java-based program.
Cygwin for Windows: For full functionality, the Windows version
requires installation either of a
Unix toolkit called Cygwin, or of some Python packages. We provide a package
for installing Cygwin on
the Download page. IMOD 4.7 should also run
reliably on more current versions of Cygwin, even on
64-bit Windows. The option to use IMOD without Cygwin is new in IMOD 4.7;
everything in IMOD will work except a few specialized C-shell scripts, but
subtomogram averaging with PEET will not work without Cygwin. We
provide Python packages on the Download page.
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: 2 GB (Linux and Mac) or 4 GB (Windows)
Operating System: Linux - Red Hat Workstation 5 or higher or Fedora 12
installation or higher (or equivalent level for Ubuntu or Suse).
Windows - Windows XP, Vista, or Win 7 or 8. Mac - OS X 10.6 or
higher (some packages should still work on OS X 10.5); only 64-bit versions for Intel
processors are now supported.
On Linux, Nvidia device drivers and OpenGL libraries from
- 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 for builds, have access to a recent
Fedora version, and can boot an Ubuntu system
- 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
IMOD Guides, Assistance and Information
The IMOD User's Guide with installation and other
- 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
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
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.
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.
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