IMOD: Difference between revisions

Revision as of 13:50, 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 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_session -e 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

@@ Line 45: / Line 45: @@
 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:
+Basic GUI usage:
   module load gui imod
   launch_gui_session -e imod
@@ Line 61: / Line 56: @@
   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
 |}}