Metadata-Version: 2.1
Name: scipion-em-imod
Version: 3.9.0
Summary: Plugin to use imod within the Scipion framework
Author-email: Scipion Team <scipion@cnb.csic.es>
License: GNU General Public License v3 (GPLv3)
Project-URL: Homepage, https://github.com/scipion-em/scipion-em-imod
Project-URL: Issues, https://github.com/scipion-em/scipion-em-imod/issues
Keywords: scipion,cryoem,cryoet,imageprocessing,scipion-3.0
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.8
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: scipion-pyworkflow>=3.11.6
Requires-Dist: scipion-em-tomo>=3.11.3

===========
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

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        :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>`_
* **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 <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>`_
* **Tilt-series alignment (batch run tomo)** : automatic tilt-series alignment using IMOD's batchruntomo `batchruntomo doc <https://bio3d.colorado.edu/imod/doc/man/batchruntomo.html>`_ wrapper made by `Team Tomo <https://teamtomo.org/teamtomo-site-archive/>`_.
* **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

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

