IMOD plugin
This plugin provides wrappers for several programs of IMOD software suite.
Installation
You will need to use 3.0+ 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
CTF correction : CTF correction of a set of input tilt-series using the IMOD procedure. More info: ctfphaseflip doc
CTF estimation (auto) : CTF estimation of a set of input tilt-series using the IMOD procedure. More info: ctfplotter doc
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
Coarse prealignment : Tilt-series cross correlation alignment based on the IMOD procedure. More info: tiltxcorr doc
Dose filter : Tilt-series dose filtering based on the IMOD procedure. More info: mtffilter doc
Etomo interactive : Simple wrapper around etomo to manually reconstruct a Tomogram. More info: etomo tutorial
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
Tilt-series alignment : Construction of a fiducial model or patch tracking and alignment of tilt-series based on the IMOD procedure. More info: tiltalign doc , model2point doc, imodtrans doc, newstack doc, ccderaser doc
Tilt-series alignment (batch run tomo) : automatic tilt-series alignment using IMOD’s batchruntomo batchruntomo doc wrapper made by Team Tomo.
Generate fiducial model : Construction of a fiducial model and alignment of tilt-series based on the IMOD procedure. More info: autofidseed doc, beadtrack doc, model2point doc
Gold bead picker 3D : 3-dimensional gold bead picker using the IMOD procedure. More info: findbeads3d doc
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
Tomo preprocess : Normalize input tomogram and change its storing formatting. More info: newstack doc, binvol doc
Tomo projection : Re-project a tomogram given a geometric description (axis and angles). More info: xyzproj doc
Tomo reconstruction : omogram reconstruction procedure based on the IMOD procedure. More info: tilt doc
X-rays eraser : Erase X-rays from aligned tilt-series based on the IMOD procedure. More info: ccderaser doc
Latest plugin versions
If you want to check the latest version and release history go to CHANGES
Installing the plugin
In order to install the plugin follow these instructions:
scipion installp -p scipion-em-imodor through the plugin manager by launching Scipion and following Configuration >> Plugins
To install in development mode
Clone or download the plugin repository
git clone -b devel https://github.com/scipion-em/scipion-em-imod.gitInstall the plugin in developer mode.
scipion installp -p local/path/to/scipion-em-imod --develIMOD 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:
IMOD_HOME = %(EM_ROOT)s/imod-4.11.25/IMODSupported versions
4.11.24, 4.11.25
References
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
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:
Status production version:
1 maintainer
Metadata
1 maintainer
Release files for scipion-em-imod 3.9.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scipion_em_imod-3.9.1.tar.gz | 133.5 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_imod-3.9.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 309.9 kB
Release files / scipion_em_imod-3.9.1.tar.gz
| Download URL | scipion_em_imod-3.9.1.tar.gz |
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| Size | 133.5 kB |
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Release files / scipion_em_imod-3.9.1-py3-none-any.whl
| Download URL | scipion_em_imod-3.9.1-py3-none-any.whl |
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| Size | 176.4 kB |
| Tags | Python 3 |
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