Difference between revisions of "IMOD"
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| − | [[Category:Software | + | [[Category:Software]][[Category:Image Processing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|imod}} | |{{#vardefine:app|imod}} | ||
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|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
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--> | --> | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_IMOD_BIN - executables directory | * HPC_IMOD_BIN - executables directory | ||
<!--Configuration--> | <!--Configuration--> | ||
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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 clip | $ launch_imod clip | ||
| − | |||
| − | |||
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Some of it is GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs | 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 | module load gui imod | ||
| − | + | launch_gui_imod | |
Connect with xpra locally using the xpra command | Connect with xpra locally using the xpra command | ||
xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713 | 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 | ||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
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<!--Policy--> | <!--Policy--> | ||
{{#if: {{#var: policy}}|==Usage Policy== | {{#if: {{#var: policy}}|==Usage Policy== | ||
| − | |||
WRITE USAGE POLICY HERE (Licensing, usage, access). | WRITE USAGE POLICY HERE (Licensing, usage, access). | ||
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|}} | |}} | ||
<!--Performance--> | <!--Performance--> | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
| − | |||
WRITE_PERFORMANCE_TESTING_RESULTS_HERE | WRITE_PERFORMANCE_TESTING_RESULTS_HERE | ||
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|}} | |}} | ||
<!--Faq--> | <!--Faq--> | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | [http://bio3d.colorado.edu/imod/paper/ 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.] | |
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|}} | |}} | ||
<!--Installation--> | <!--Installation--> | ||
Latest revision as of 14:42, 14 December 2022
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_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: