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.

• IMOD Guides

• Module Name: IMOD (see the modules page for more information)
• Environment variables set: IMOD_PROCESSORS is set to the number of CPUs allocated.
• Example files in /usr/local/apps/IMOD/imod_data.tar.gz

Allocate an interactive session and run the program. Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=4 --mem=10g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ module load IMOD
[+] Loading IMOD 4.11.5 . Running with 4 CPUs

# note: loading the module will cause the environment variable IMOD_PROCESSORS to be set to the number of 
#   allocated CPUs. i.e. 4 in this example.

[user@cn3144]$ tar xvzf /usr/local/apps/IMOD/imod_data.tar.gz

[user@cn3144]$ mrc2tif imod_data/golgi.mrc imod_data/golgi.tif
Writing TIFF images. ................................

[user@cn3144]$ newstack golgi.mrc golgi.st

 RO image file on unit   1 : golgi.mrc     Size=       2049 K

                    This is a byte-swapped file.

                    This file has an old-style MRC header.

 Number of columns, rows, sections .....     256     256      32
 Map mode ..............................    0   (byte)
 Start cols, rows, sects, grid x,y,z ...    0     0     0     256    256     32
 Pixel spacing (Angstroms)..............   1.000      1.000      1.000
 Cell angles ...........................   90.000   90.000   90.000
 Fast, medium, slow axes ...............    X    Y    Z
 Origin on x,y,z .......................    0.000       0.000       0.000
 Minimum density .......................   17.000
 Maximum density .......................   195.00
 Mean density ..........................   83.733
 tilt angles (original,current) ........   0.0   0.0   0.0   0.0   0.0   0.0
 Space group,# extra bytes,idtype,lens .        0        0        0        0
[...]      
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

To run etomo or other IMOD graphics applications, you need a graphics connection to Biowulf. We recommend NX for Windows, Mac or Linux.

Once you have an NX connection to Biowulf, start an interactive session, load the IMOD module, and then run etomo. Sample session following the etomoTutorial.

If you are having trouble seeing the entire etomo window, here is an NX tip: move your mouse over your name in the top right corner of the NX window. It will appear to 'peel back'. You can then see the NX options: select 'Display' and then 'Resize remote display'.

You should then be able to work through the entire tutorial.

Create a batch input file (e.g. IMOD.sh). For example:

#!/bin/bash
set -e
module load IMOD

cd /data/$USER/myimagedir
tif2mrc cell*.tif cell.mrc
newstack cell*.mrc cell.st 

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] IMOD.sh

Create a swarmfile (e.g. IMOD.swarm). For example:

newstack cell*.mrc
newstack cell2*.mrc
newstack cell3*.mrc

Submit this job using the swarm command.

swarm -f IMOD.swarm [-g #] [-t #] --module IMOD