Package: scipion-em-imod
This plugin provides wrappers for several programs ofIMODsoftware suite.Current developmentThis plugin is currently inBETAmode.InstallationYou will need to use3.0+version of Scipion to be able to run these protocols.ProtocolsApply transformation: Compute the interpolated tilt-series from its transform matrix. More info:newstack docAutomatic CTF estimation:  CTF estimation of a set of input tilt-series using the IMOD procedure. More info:ctfplotter docCTF correction: CTF correction of a set of input tilt-series using the IMOD procedure. More info:ctfphaseflip docDose filter: Tilt-series dose filtering based on the IMOD procedure. More info:mtffilter docEtomo interactive: Simple wrapper around etomo to manually reconstruct a Tomogram. More info:etomo tutorialExclude 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:hereFiducial alignment: Construction of a fiducial model and alignment of tilt-series based on the IMOD procedure. More info:tiltalign doc,model2point doc,imodtrans doc,newstack doc,ccderaser docGenerate fiducial model: Construction of a fiducial model and alignment of tilt-series based on the IMOD procedure. More info:autofidseed doc,beadtrack doc,model2point docGold bead picker 3D: 3-dimensional gold bead picker using the IMOD procedure. More info:findbeads3d docImport tomo CTFs:  Protocol to import estimations of CTF series from tilt-series into Scipion.Import transformation matrix: Import the transformation matrices assigned to an input set of tilt-seriesManual CTF estimation: 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 docTilt-series preprocess: Normalize input tilt-series and change its storing formatting. More info:newstack docTomo preprocess: Normalize input tomogram and change its storing formatting. More info:newstack doc,binvol docTomo projection: Re-project a tomogram given a geometric description (axis and angles). More info:xyzproj docTomo reconstruction: omogram reconstruction procedure based on the IMOD procedure. More info:tilt docCoarse prealignment: Tilt-series cross correlation alignment based on the IMOD procedure. More info:tiltxcorr docX-rays eraser: Erase X-rays from aligned tilt-series based on the IMOD procedure. More info:ccderaser docLatest plugin versionsIf you want to check the latest version and release history go toCHANGESInstalling the pluginIn order to install the plugin follow these instructions:scipion installp -p scipion-em-imodor through theplugin managerby launching Scipion and followingConfiguration>>PluginsTo install in development modeClone or download the plugin repositorygit clone 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 issoftware/em/imod-4.11.24/IMOD, if you want to change it, setIMOD_HOMEinscipion.conffile 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 executingscipion test--show--grepimodChanging the binning level for 3dmodFor quick visualization purposes, it can be useful to bin images and tomograms on the fly using theImodViewerprovided by this plugin (i.e.3dmod). For that, the user can define theIMOD_VIEWER_BINNINGenvironment variable inscipion.confas in the following example:IMOD_HOME = %(EM_ROOT)s/imod-4.11.24/IMOD
IMOD_VIEWER_BINNING = 8Supported versions4.11.7, 4.11.20, 4.11.24ReferencesJames 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.1996.0013David 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.2016.07.011Buildbot statusStatus devel version:Status production version: