Metadata-Version: 2.1
Name: scipion-em-imod
Version: 3.1.5
Summary: Plugin to use some of the Tomography tools from IMOD in Scipion
Home-page: https://github.com/scipion-em/scipion-em-imod
Author: J.M. De la Rosa, Federico P. de Isidro Gomez
Author-email: delarosatrevin@scilifelab.se, fp.deisidro@cnb.csic.es
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/scipion-em/scipion-em-imod/issues
Project-URL: Source, https://github.com/scipion-em/scipion-em-imod/
Description: ===========
        IMOD plugin
        ===========
        
        This plugin provides wrappers for several programs of `IMOD <https://bio3d.colorado.edu/imod/>`_ software suite.
        
        .. image:: https://img.shields.io/pypi/v/scipion-em-imod.svg
                :target: https://pypi.python.org/pypi/scipion-em-imod
                :alt: PyPI release
        
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                :alt: License
        
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                :target: https://pypi.python.org/pypi/scipion-em-imod
                :alt: Supported Python versions
        
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        .. image:: https://img.shields.io/pypi/dm/scipion-em-imod
                :target: https://pypi.python.org/pypi/scipion-em-imod
                :alt: Downloads
        
        Current development
        -------------------
        
        This plugin is currently in **BETA** mode.
        
        
        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>`__
        * **Automatic CTF estimation** :  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 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>`_
        * **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 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-series
        * **Manual 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 doc <https://bio3d.colorado.edu/imod/doc/man/ctfplotter.html>`_
        * **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>`_
        * **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>`_
        * **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 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``
        
        Supported versions
        ------------------
        
        4.11.7, 4.11.20, 4.11.24
        
        
        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:
        
        .. image:: http://scipion-test.cnb.csic.es:9980/badges/imod_devel.svg
        
        
        Status production version:
        
        .. image:: http://scipion-test.cnb.csic.es:9980/badges/imod_prod.svg
        
        
Keywords: scipion imod electron-microscopy cryo-em cryo-tomography subtomogram-averaging structural-biology image-processing scipion-3.0
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/x-rst
