=========== IMOD plugin

This plugin provides wrappers for several programs of IMOD <https://bio3d.colorado.edu/imod/>_ software suite.

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Installation

You will need to use 3.0+ <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html>_ version of Scipion to be able to run these protocols.

Protocols

• Apply transformation : Compute the interpolated tilt-series from its transform matrix. More info: newstack doc <https://bio3d.colorado.edu/imod/doc/man/newstack.html>__
• CTF correction : CTF correction of a set of input tilt-series using the IMOD procedure. More info: ctfphaseflip doc <https://bio3d.colorado.edu/imod/doc/man/ctfphaseflip.html>_
• CTF estimation (auto) : CTF estimation of a set of input tilt-series using the IMOD procedure. More info: ctfplotter doc <https://bio3d.colorado.edu/imod/doc/man/ctfplotter.html>_
• CTF estimation (manual) : CTF estimation of a set of input tilt-series using the IMOD procedure. Runs the protocol through the interactive GUI. The resulting defocus values MUST BE SAVED manually by the user. More info: ctfplotter doc <https://bio3d.colorado.edu/imod/doc/man/ctfplotter.html>_
• Coarse prealignment : Tilt-series cross correlation alignment based on the IMOD procedure. More info: tiltxcorr doc <https://bio3d.colorado.edu/imod/doc/man/tiltxcorr.html>_
• Dose filter : Tilt-series dose filtering based on the IMOD procedure. More info: mtffilter doc <https://bio3d.colorado.edu/imod/doc/man/mtffilter.html>_
• Etomo interactive : Simple wrapper around etomo to manually reconstruct a Tomogram. More info: etomo tutorial <https://bio3d.colorado.edu/imod/doc/etomoTutorial.html>_
• Exclude views : excludeviews - Reversibly remove views from a tilt series stack. If you use this protocol, make sure tis output tilt series is use for everything else CTF estimation, per particle per tilt, tomogram reconstruction....More info: here <https://bio3d.colorado.edu/imod/doc/man/excludeviews.html>_
• Fiducial alignment : Construction of a fiducial model and alignment of tilt-series based on the IMOD procedure. More info: tiltalign doc <https://bio3d.colorado.edu/imod/doc/man/tiltalign.html> , model2point doc <https://bio3d.colorado.edu/imod/doc/man/model2point.html>, imodtrans doc <https://bio3d.colorado.edu/imod/doc/man/imodtrans.html>_, newstack doc <https://bio3d.colorado.edu/imod/doc/man/newstack.html>_, ccderaser doc <https://bio3d.colorado.edu/imod/doc/man/ccderaser.html>
• Generate fiducial model : Construction of a fiducial model and alignment of tilt-series based on the IMOD procedure. More info: autofidseed doc <https://bio3d.colorado.edu/imod/doc/man/autofidseed.html>, beadtrack doc <https://bio3d.colorado.edu/imod/doc/man/beadtrack.html>, model2point doc <https://bio3d.colorado.edu/imod/doc/man/model2point.html>_
• Gold bead picker 3D : 3-dimensional gold bead picker using the IMOD procedure. More info: findbeads3d doc <https://bio3d.colorado.edu/imod/doc/man/findbeads3d.html>_
• Import transformation matrix : Import the transformation matrices assigned to an input set of tilt-series
• Tilt-series preprocess : Normalize input tilt-series and change its storing formatting. More info: newstack doc <https://bio3d.colorado.edu/imod/doc/man/newstack.html>__
• Tomo preprocess : Normalize input tomogram and change its storing formatting. More info: newstack doc <https://bio3D.colorado.edu/imod/doc/newstack.html>_, binvol doc <https://bio3D.colorado.edu/imod/doc/binvol.html>
• Tomo projection : Re-project a tomogram given a geometric description (axis and angles). More info: xyzproj doc <https://bio3d.colorado.edu/imod/doc/man/xyzproj.html>_
• Tomo reconstruction : omogram reconstruction procedure based on the IMOD procedure. More info: tilt doc <https://bio3d.colorado.edu/imod/doc/man/tilt.html>_
• X-rays eraser : Erase X-rays from aligned tilt-series based on the IMOD procedure. More info: ccderaser doc <https://bio3d.colorado.edu/imod/doc/man/ccderaser.html>_

Latest plugin versions

If you want to check the latest version and release history go to CHANGES <https://github.com/scipion-em/scipion-em-imod/imod/blob/master/CHANGES.txt>_

Installing the plugin

In order to install the plugin follow these instructions:

.. code-block::

scipion installp -p scipion-em-imod

or through the plugin manager by launching Scipion and following Configuration >> Plugins

To install in development mode

Clone or download the plugin repository

.. code-block::

git clone -b devel https://github.com/scipion-em/scipion-em-imod.git

Install the plugin in developer mode.

.. code-block::

scipion installp -p local/path/to/scipion-em-imod --devel

IMOD binaries will be downloaded and installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/imod-4.11.24/IMOD, if you want to change it, set IMOD_HOME in scipion.conf file to the folder where the IMOD is installed.

To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing scipion test --show --grep imod

Changing the binning level for 3dmod

For quick visualization purposes, it can be useful to bin images and tomograms on the fly using the ImodViewer provided by this plugin (i.e. 3dmod). For that, the user can define the IMOD_VIEWER_BINNING environment variable in scipion.conf as in the following example:

.. code-block:: [PLUGINS]

    IMOD_HOME = %(EM_ROOT)s/imod-4.11.25/IMOD
    IMOD_VIEWER_BINNING = 8

Supported versions

4.11.24, 4.11.25

References

1. James R. Kremer, David N. Mastronarde, J.Richard McIntosh. Computer Visualization of Three-Dimensional Image Data Using IMOD. Journal of Structural Biology, Volume 116, Issue 1, 1996, Pages 71-76. https://doi.org/10.1006/jsbi.1996.0013
2. David N. Mastronarde, Susannah R. Held. Automated tilt series alignment and tomographic reconstruction in IMOD. Journal of Structural Biology, Volume 197, Issue 2, 2017, Pages 102-113, ISSN 1047-8477. https://doi.org/10.1016/j.jsb.2016.07.011

Buildbot status

Status devel version:

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Status production version:

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