=========================
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
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"description": "=========================\nScipion plugin for Tomo3D\n=========================\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-tomo3d.svg\n :target: https://pypi.python.org/pypi/scipion-em-tomo3d\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-tomo3d.svg\n :target: https://pypi.python.org/pypi/scipion-em-tomo3d\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-tomo3d.svg\n :target: https://pypi.python.org/pypi/scipion-em-tomo3d\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-tomo3d\n :target: https://pypi.python.org/pypi/scipion-em-tomo3d\n :alt: Downloads\n\nThis plugin allows to use some of the software packages from 3demimageprocessing_ within the Scipion framework.\n**The binaries for the plugin MUST be downloaded manually**:\n\n============\nInstallation\n============\n\nThe plugin can be installed in user (stable) or developer (latest, may be unstable) mode:\n\n**1. User (stable) version:**:\n\n.. code-block::\n\n scipion installp -p scipion-em-tomo3d\n\n**2. Developer (latest, may be unstable) version:**:\n\n* Clone the source code repository:\n\n.. code-block::\n\n git clone https://github.com/scipion-em/scipion-em-tomo3d.git\n\n* Install:\n\n.. code-block::\n\n scipion3 installp -p local/path/to/scipion-em-tomo3d --devel\n\n=========\nProtocols\n=========\nThe integrated protocols are:\n\n1. tomo3d - denoise tomograms\n\n2. tomo3d - reconstruct tomograms\n\n=====\nTests\n=====\n\nThe installation can be checked out running some tests:\n\n.. code-block::\n\n scipion3 tests tomo3d.tests.test_protocol_reconstruct_tomogram\n\n.. code-block::\n\n scipion3 tests tomo3d.tests.test_protocol_denoise_tomogram\n\n\n==========\nReferences\n==========\n\n* `Fast tomographic reconstruction on multicore computers. <https://doi.org/10.1093/bioinformatics/btq692>`_\n J.I. Agulleiro, J.J. Fernandez. Bioinformatics 27:582-583, 2011.\n\n* `Tomo3D 2.0 \u2013 Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction. <https://doi.org/10.1016/j.jsb.2014.11.009>`_\n J.I. Agulleiro, J.J. Fernandez. Journal of Structural Biology 189:147-152, 2015.\n\n* `TOMOBFLOW: feature-preserving noise filtering for electron tomography. <https://doi.org/10.1186/1471-2105-10-178>`_\n J.J. Fernandez. BMC Bioinformatics 2009, 10:178.\n\n* `TomoEED: Fast Edge-Enhancing Denoising of Tomographic Volumes. <https://doi.org/10.1093/bioinformatics/bty435>`_\n J.J. Moreno, A. Martinez-Sanchez, J.A. Martinez, E.M. Garzon, J.J. Fernandez. Bioinformatics 34:3776-3778, 2018. \n\n===================\nContact information\n===================\n\nIf you experiment any problem, please contact us here: scipion-users@lists.sourceforge.net, scipion@cnb.csic.es or open an issue_.\n\nWe'll be pleased to help.\n\n*Scipion Team*\n\n\n.. _3demimageprocessing: https://sites.google.com/site/3demimageprocessing/\n.. _tomo3d: https://sites.google.com/site/3demimageprocessing/tomo3d\n.. _tomowarpalign: https://sites.google.com/site/3demimageprocessing/tomoalign\n.. _tomobflow: https://sites.google.com/site/3demimageprocessing/tomobflow\n.. _tomoeed: https://sites.google.com/site/3demimageprocessing/tomoeed\n.. _issue: https://github.com/scipion-em/scipion-em-tomo3d/issues\n\n\n",
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