=============
cisTEM plugin
=============
This plugin provides wrappers for several programs of `cisTEM <https://cistem.org>`_ software suite.
.. image:: https://img.shields.io/pypi/v/scipion-em-cistem.svg
:target: https://pypi.python.org/pypi/scipion-em-cistem
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-cistem.svg
:target: https://pypi.python.org/pypi/scipion-em-cistem
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-cistem.svg
:target: https://pypi.python.org/pypi/scipion-em-cistem
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-cistem?server=https%3A%2F%2Fsonarcloud.io
:target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-cistem
:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/dm/scipion-em-cistem
:target: https://pypi.python.org/pypi/scipion-em-cistem
:alt: Downloads
Installation
------------
You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
a) Stable version
.. code-block::
scipion installp -p scipion-em-cistem
b) Developer's version
* download repository
.. code-block::
git clone -b devel https://github.com/scipion-em/scipion-em-cistem.git
* install
.. code-block::
scipion installp -p /path/to/scipion-em-cistem --devel
**Important:** Starting from plugin v3.9, the config variables have been renamed. See: `scipion3 config -p cistem`
cisTEM binaries will be installed automatically with the plugin, but you can also link an existing installation.
* Default installation path assumed is ``software/em/cistem-1.0.0-beta``, if you want to change it, set *CISTEM_HOME* in ``scipion.conf`` file pointing to the folder where the cisTEM is installed.
* It's possible to use CTFFIND installed separately from cisTEM by defining *CTFFIND_HOME* variable in ``scipion.conf``. Setting this value will have the priority over Ctffind inside cisTEM.
A complete list of tests can be seen by executing ``scipion test --show --grep cistem``
Supported versions
------------------
* 1.0.0-beta (cistem)
* 4.1.13, 4.1.14 (ctffind4)
* 5.0 (ctffind5)
Licenses
--------
* cistem binaries are distributed under `The Janelia Research Campus Software License 1.2 license <http://license.janelia.org/license/janelia_license_1_2.html>`_
* ctffind4 binaries are distributed under `The Janelia Research Campus Software License 1.1 license <https://www.janelia.org/node/47808>`_
* ctffind5 binaries are distributed under `The Janelia Research Campus Software License 1.2 license <http://license.janelia.org/license/janelia_license_1_2.html>`_
Protocols
---------
* ctffind
* import tomo CTFs
* tilt-series ctffind
* unblur
* find particles
* classify 2D
References
----------
1. Johannes Elferich, Lingli Kong, Ximena Zottig, Nikolaus Grigorieff. (2024) CTFFIND5 provides improved insight into quality, tilt and thickness of TEM samples. bioRxiv 2024.02.26.582023; doi: https://doi.org/10.1101/2024.02.26.582023
2. Timothy Grant and Alexis Rohou and Nikolaus Grigorieff. (2018) cisTEM, user-friendly software for single-particle image processing. eLife 7:e35383.
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