Difference between revisions of "IMOD"
| Line 45: | Line 45: | ||
IMOD is installed in a container. Use the 'launch_imod' command to access IMOD executables: | IMOD is installed in a container. Use the 'launch_imod' command to access IMOD executables: | ||
| − | $ launch_imod | + | $ launch_imod imod |
or | or | ||
| − | $ launch_imod | + | $ launch_imod clip |
To see the list of all available executables in IMOD use the following command: | To see the list of all available executables in IMOD use the following command: | ||
$ launch_imod ls $HPC_IMOD_BIN | $ launch_imod ls $HPC_IMOD_BIN | ||
| + | |||
| + | Some of it is GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs | ||
| + | |||
| + | Basic usage: | ||
| + | module load gui imod | ||
| + | launch_gui_session -e imod | ||
| + | |||
| + | Connect with xpra locally using the xpra command | ||
| + | xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713 | ||
Revision as of 13:49, 21 October 2016
Description
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 imod
or
$ launch_imod clip
To see the list of all available executables in IMOD use the following command:
$ launch_imod ls $HPC_IMOD_BIN
Some of it is GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs
Basic usage:
module load gui imod launch_gui_session -e imod
Connect with xpra locally using the xpra command
xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713