Metadata-Version: 2.1
Name: scipion-em-tomo3d
Version: 3.1.4
Summary: tomo3d and other software at https://sites.google.com/site/3demimageprocessing/Home ready to use in scipion.
Home-page: https://github.com/scipion-em/scipion-em-tomo3d
Author: I2PC
Author-email: scipion@cnb.csic.es
License: UNKNOWN
Keywords: scipion cryoem imageprocessing 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

=========================
Scipion plugin for Tomo3D
=========================

.. image:: https://img.shields.io/pypi/v/scipion-em-tomo3d.svg
        :target: https://pypi.python.org/pypi/scipion-em-tomo3d
        :alt: PyPI release

.. image:: https://img.shields.io/pypi/l/scipion-em-tomo3d.svg
        :target: https://pypi.python.org/pypi/scipion-em-tomo3d
        :alt: License

.. image:: https://img.shields.io/pypi/pyversions/scipion-em-tomo3d.svg
        :target: https://pypi.python.org/pypi/scipion-em-tomo3d
        :alt: Supported Python versions

.. image:: https://img.shields.io/pypi/dm/scipion-em-tomo3d
        :target: https://pypi.python.org/pypi/scipion-em-tomo3d
        :alt: Downloads

This plugin allows to use some of the software packages from 3demimageprocessing_ within the Scipion framework.
**The binaries for the plugin MUST be downloaded manually**:

============
Installation
============

The plugin can be installed in user (stable) or developer (latest, may be unstable) mode:

**1. User (stable) version:**:

.. code-block::

    scipion installp -p scipion-em-tomo3d

**2. Developer (latest, may be unstable) version:**:

* Clone the source code repository:

.. code-block::

    git clone https://github.com/scipion-em/scipion-em-tomo3d.git

* Install:

.. code-block::

    scipion3 installp -p local/path/to/scipion-em-tomo3d --devel

=========
Protocols
=========
The integrated protocols are:

1. tomo3d - denoise tomograms

2. tomo3d - reconstruct tomograms

=====
Tests
=====

The installation can be checked out running some tests:

.. code-block::

     scipion3 tests tomo3d.tests.test_protocol_reconstruct_tomogram

.. code-block::

    scipion3 tests tomo3d.tests.test_protocol_denoise_tomogram


==========
References
==========

* `Fast tomographic reconstruction on multicore computers. <https://doi.org/10.1093/bioinformatics/btq692>`_
  J.I. Agulleiro, J.J. Fernandez. Bioinformatics 27:582-583, 2011.

* `Tomo3D 2.0 – Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction. <https://doi.org/10.1016/j.jsb.2014.11.009>`_
  J.I. Agulleiro, J.J. Fernandez. Journal of Structural Biology 189:147-152, 2015.

* `TOMOBFLOW: feature-preserving noise filtering for electron tomography. <https://doi.org/10.1186/1471-2105-10-178>`_
  J.J. Fernandez. BMC Bioinformatics 2009, 10:178.

* `TomoEED: Fast Edge-Enhancing Denoising of Tomographic Volumes. <https://doi.org/10.1093/bioinformatics/bty435>`_
  J.J. Moreno, A. Martinez-Sanchez, J.A. Martinez, E.M. Garzon, J.J. Fernandez. Bioinformatics 34:3776-3778, 2018. 

===================
Contact information
===================

If you experiment any problem, please contact us here: scipion-users@lists.sourceforge.net, scipion@cnb.csic.es or open an issue_.

We'll be pleased to help.

*Scipion Team*


.. _3demimageprocessing: https://sites.google.com/site/3demimageprocessing/
.. _tomo3d: https://sites.google.com/site/3demimageprocessing/tomo3d
.. _tomowarpalign: https://sites.google.com/site/3demimageprocessing/tomoalign
.. _tomobflow: https://sites.google.com/site/3demimageprocessing/tomobflow
.. _tomoeed: https://sites.google.com/site/3demimageprocessing/tomoeed
.. _issue: https://github.com/scipion-em/scipion-em-tomo3d/issues


