===========
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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:target: https://pypi.python.org/pypi/scipion-em-imod
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-imod.svg
:target: https://pypi.python.org/pypi/scipion-em-imod
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-imod?server=https%3A%2F%2Fsonarcloud.io
:target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-imod
:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/dm/scipion-em-imod
:target: https://pypi.python.org/pypi/scipion-em-imod
:alt: Downloads
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:
.. 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
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More info: `newstack doc <https://bio3d.colorado.edu/imod/doc/man/newstack.html>`__\n* **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>`_\n* **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>`_\n* **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>`_\n* **Coarse prealignment** : Tilt-series cross correlation alignment based on the IMOD procedure. 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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>`_\n* **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>`_\n* **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>`_\n* **Import transformation matrix** : Import the transformation matrices assigned to an input set of tilt-series\n* **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>`__\n* **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>`_\n* **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>`_\n* **Tomo reconstruction** : omogram reconstruction procedure based on the IMOD procedure. More info: `tilt doc <https://bio3d.colorado.edu/imod/doc/man/tilt.html>`_\n* **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>`_\n\n**Latest plugin versions**\n==========================\n\nIf 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>`_\n\n\n**Installing the plugin**\n=========================\n\nIn order to install the plugin follow these instructions:\n\n.. code-block::\n\n scipion installp -p scipion-em-imod\n\n\nor through the **plugin manager** by launching Scipion and following **Configuration** >> **Plugins**\n\n\n**To install in development mode**\n\nClone or download the plugin repository\n\n.. code-block::\n\n git clone -b devel https://github.com/scipion-em/scipion-em-imod.git\n\nInstall the plugin in developer mode.\n\n.. code-block::\n\n scipion installp -p local/path/to/scipion-em-imod --devel\n\n\nIMOD binaries will be downloaded and installed automatically with the plugin, but you can also link an existing installation. 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