The IMOD Home Page (original) (raw)

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, Suraj Khochare, and John Heumann at the University of Colorado.

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) 1994-2024 by the Regents of the University of Colorado. Other contributors are acknowledged in our Copyright and Credits statement.

IMOD 5.1 Is Now Available for Linux, Windows, and Mac OS

DOWNLOAD IMOD 5.1
Download Alpha or Beta Development Versions (IMOD 5.2.x)
[Release Notes](#Release Notes)
Hardware and Operating System Requirements
IMOD Guides, Assistance and Information
IMOD Discussion and Mailing Lists (subscribing and unsubscribing)
IMOD Source Code
SerialEM Tilt Series Acquisition Software

Release Notes

IMOD 5.1 contains a variety of major functional enhancements plus the usual assortment of bug fixes and minor additions. The highlights of this version include:

• The tilt series alignment program can estimate how well a solution with some points left out predicts the location of those points; using this estimate, the selection of parameters can be optimized to avoid fitting to too many variables
• The program for determining the CTF parameters for tilt series images was enhanced with:
  • Automatic tuning of the power spectrum sampling and the frequency fitting range
  • Automatic truncation of the fitting range as the signal weakens at higher tilt
  • Initial scanning over a wide defocus range to find the starting defocus value
  • Ability to find and set a tilt angle offset to compensate for tilted specimens
• Etomo has new interfaces for:
  • Tomogram reconstruction with correction in 3D for microscope CTF
  • Generating subtomograms at particle positions, also with 3D CTF correction
  • Building a tomogram from an alternative tilt series stack with identical alignment to the processed stack (e.g., multiple STEM channels or stacks summed from even and odd frames)
  • Aligning camera frames from a tilt series to produce a tilt series ready to process
• The panel in Etomo for "squeezing" a volume was changed to allow antialiased volume reduction and filtering with a low-pass or deconvolution filter
• The batch reconstruction interface in Etomo now allows processing multiple data sets in parallel and running on a cluster
• The tomogram generation program can reconstruct directly from raw tilt series images; this option is incorporated in the Etomo 3D CTF and subtomogram interfaces
• The program for blending montaged images can now correct for intensity gradients and variations between images, and has new features to align tiles more reliably in periodic specimens, including EM grid maps

Here is the complete list of changes in IMOD 5.1

Changes in previous versions:

• IMOD 4.11.25.
• IMOD 4.11
• IMOD 4.9.12.
• IMOD 4.9.
• IMOD 4.7.15.
• IMOD 4.7
• IMOD 4.5.8
• IMOD 4.5

Hardware and Operating System Requirements

Java for Etomo: The Etomo program for building tomograms requires a Java run-time environment. An OpenJDK version of Java should be used unless you have a license for Oracle Java. For Linux, such versions are generally available or installed by default with current distributions. Otherwise, a package can be obtained from Adoptium; see the IMOD Guide for details.

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 packages for installing Cygwin on the Download page. When using IMOD without Cygwin, 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 to work on the display.

The recommended minimal configuration for running the IMOD software is:

• Processor: Any modern Intel or AMD processor.
• Video Cards: Any relatively modern NVIDIA-based card (2 GB or higher cards preferred); AMD cards also work for graphics display but cannot be used for GPU computation.
• Minimum recommended memory size: 16 GB; more depending on size of data to be processed and viewed.
• Operating System: Linux - Red Hat Workstation 8 or higher (or equivalent level for Fedora, Ubuntu or Suse).Windows - Windows 10 or 11 (but IMOD will still run on XP, Vista, 7, and 8). Mac - OS X 10.14 or higher.
• On Linux, NVIDIA device drivers and OpenGL libraries fromNVIDIA

Notes:

• Graphics Performance. 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.
• 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 8 but still run Red Hat 7 for builds; we have virtual machines with Red Hat 9 and many Ubuntu LTS versions.
• Use of a GPU and Multiple CPU Cores The GPU can be used in the programs for backprojection/reprojection, CTF correction, and alignment of camera movie frames. Many of the most time-consuming operations can take advantage of multiple CPU cores.
• 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 64 GB is recommended.
• Consider consulting the IMOD discussion list for advice about what computer capability will meet your particular needs.

IMOD Guides, Assistance and Information

• The IMOD User's Guide with installation and other general information.
• Tomography Resources
  • A Tomography Guide, with detailed instructions on building tomograms with the IMOD package.
  • A Tutorial for building a dual-axis tomogram with Etomo, and a sample data set.
  • A tutorial on reconstructing a cellular cryotomogram with fiducials, and a sample data set.
  • A tutorial on reconstructing a high-resolution cryotomogram with fiducials, and a sample data set from a study of HIV VLP's, the same set used for the CTF correction tutorial below.
  • A tutorial on reconstructing a frozen-hydrated section with patch tracking, and a sample data set.
  • A guide to joining tomograms from serial sections.
  • A tutorial for joining serial section tomograms with Etomo, and a sample data set.
  • A Batch Reconstruction Guide, with details on using the interface for batch processing of tilt series in Etomo.
  • A tutorial for using the batch interface, which uses the binned and unbinned Etomo tutorial data sets.
  • A tutorial on using the SIRT reconstruction and Filter Trials interfaces, which uses the same data set from an UltraScan camera as the CTF tutorial.
  • Lectures, videos and practice data sets from a 5-day workshop on IMOD and PEET at Rocky Mountain Laboratories in June 2017.
  • Tutorial videos on YouTube.
• Resources on CTF Correction
  • A tutorial on finding defocus for CTF correction, with sample data sets from a study of HIV VLP's, from a K2 camera, from an UltraScan camera, and from a DE-12 camera.
  • The full Guide to Ctfplotter
  • A lecture on CTF correction from a workshop in 2017, before the current version of Ctfplotter.
  • The Powerpoint slides from a 2019 workshop, which covers finding astigmatism and some other newer features of Ctfplotter.
• Modeling Resources
  • The Introduction to 3dmod, which provides a comprehensive tour of the major features of the 3dmod image display and modeling program.
  • A modeling tutorial by Cindi Schwartz, and a small example tomogram that it uses. Unpack this file with the command:
    imoduntar ivemcut.tar.bz2
  • Example images of IMOD model renderings.
  • Sample data files that can be used to experiment with IMOD are available in a gzipped tar archive: imod_data.tar.gz
• A guide to aligning serial section images and blending montages.
• A guide to aligning movie frames in Etomo using Alignframes.
• A tutorial on filtering with Nonlinear Anisotropic Diffusion (NAD), and a sample tomogram.
• 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.
• Beta documentation: Links to all documentation in the latest development version of IMOD, updated nightly.
• 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. For batch reconstruction and recently automated features, see Mastronarde, D.N. and Held, S.R. (2017) Automated tilt series alignment and tomographic reconstruction in IMOD. J. Struct. Biol. 197:102-113. For CTF correction, see Mastronarde, D.N. (2024) Accurate, automatic determination of astigmatism and phase with Ctfplotter in IMOD. J. Struct Biol. 216:108057.
• Instructions for joining the IMOD discussion list and signing up on a separate mailing list.
• Source code is also available.
• Matlab code for accessing IMOD models and MRC image files is available in the PEET package.