IMOD

Description

imod website  

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 University of Colorado.

Required Modules

Serial

• imod

System Variables

• HPC_{{#uppercase:imod}}_DIR - installation directory
• HPC_IMOD_BIN - executables directory

Additional Information

IMOD is installed in a container. Use the 'launch_imod' command to access IMOD executables:

$ launch_imod clip

Some of it is GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs

Basic GUI usage:

module load gui imod
launch_gui_imod

Connect with xpra locally using the xpra command

xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713

To see the list of all available executables in IMOD use the following command:

$ launch_imod ls $HPC_IMOD_BIN

Citation

If you publish research that uses imod you have to cite it as follows:

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.