IMOD

Overview

IMOD is an EM tomography software suite that has been developed by the Boulder Laboratory. Although basically runs through command line interfaces and scripts, most users learn to use IMOD using its GUI called eTomo.

Contents

Using IMOD

Things you will need:

A tilt series aka your dataset acquired on an EM
A .rawtlt file or knowledge of the tilt angles that were acquired
A computer that has IMOD installed (NCMIR personnel click here for list of machines to log into)

Things that are helpful:

Size of gold fiducial markers
Magnification

The Boulder Laboratory has an easy to follow tutorial found here and thus, no step-by-step instruction will be provided on these pages.

NCMIR STAFF: Please remember not to download the tutorial dataset to your home directory but instead to one of the network drives. See a network admin or your supervisor where data should be saved.

Useful IMOD hotkeys

No information at this time

Conceptual steps of IMOD backprojection

Making the .rawtlt file
Pre-processing

Coarse Alignment
Fiducial Model Generation
Fine Alignment
Tomogram Positioning
Final Aligned Stack
Tomogram Generation
If reconstructing a double-tilt dataset, the next few steps apply:
Tomogram Combination
Post-processing
Clean Up

IMOD files: what they all mean

FAQ

How do I learn to use IMOD?
I type etomo in a terminal window but it won't start up!
Can I use IMOD on my home computer?
The contrast on my .preali file looks strange or blown out!
How many gold fiducials should I try to track?
The fiducials aren't tracking from the .seed file! Why?!
Help! I can't get my residual error to the levels the tutorial had! What's an "acceptable" residual error level?
What can I do to lower my residual error?

Common Error Messages