Difference between revisions of "IMOD"

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[[Category:Software]][[Category:3D Modeling]][[Category:Image Reconstruction]]
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[[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-->
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|{{#vardefine:citation|1}}      <!--CITATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|}
 
|}
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-->
 
-->
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* HPC_IMOD_BIN - executables directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==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 3dmod
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  $ launch_imod clip
or
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  $ launch_imod etomo
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Some of it is GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs
 +
 
 +
Basic GUI usage:
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module load gui imod
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launch_gui_imod
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 +
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:
 
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  
 
 
 
|}}
 
|}}
 
<!--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).
 
 
|}}
 
|}}
 
<!--Performance-->
 
<!--Performance-->
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
 
 
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 
 
|}}
 
|}}
 
<!--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:
  
WRITE_CITATION_HERE
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[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.]
 
 
 
|}}
 
|}}
 
<!--Installation-->
 
<!--Installation-->

Latest revision as of 14:42, 14 December 2022

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_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.