=========================
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
Raw data
{
"_id": null,
"home_page": "https://github.com/scipion-em/scipion-em-tomo3d",
"name": "scipion-em-tomo3d",
"maintainer": null,
"docs_url": null,
"requires_python": null,
"maintainer_email": null,
"keywords": "scipion cryoem imageprocessing scipion-3.0",
"author": "I2PC",
"author_email": "scipion@cnb.csic.es",
"download_url": "https://files.pythonhosted.org/packages/c3/b9/caa468dab576021ee73907b2fefc314818a02a8dc7d7c29c46f88812eb2b/scipion-em-tomo3d-3.1.3.tar.gz",
"platform": null,
"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",
"bugtrack_url": null,
"license": null,
"summary": "tomo3d and other software at https://sites.google.com/site/3demimageprocessing/Home ready to use in scipion.",
"version": "3.1.3",
"project_urls": {
"Homepage": "https://github.com/scipion-em/scipion-em-tomo3d"
},
"split_keywords": [
"scipion",
"cryoem",
"imageprocessing",
"scipion-3.0"
],
"urls": [
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "a12d498a056cfcef0ec4b0c77e469a946d6b622d92e3b50bc21d799d5dc173b7",
"md5": "d09a3d37c74e016bf504b5452d1fde9a",
"sha256": "de499e2db2785f6fe2e590ccd6c0a64a105984dcacdb5d4e2f88ee1e2e9c7dc4"
},
"downloads": -1,
"filename": "scipion_em_tomo3d-3.1.3-py3-none-any.whl",
"has_sig": false,
"md5_digest": "d09a3d37c74e016bf504b5452d1fde9a",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 42821,
"upload_time": "2024-10-03T13:26:14",
"upload_time_iso_8601": "2024-10-03T13:26:14.816181Z",
"url": "https://files.pythonhosted.org/packages/a1/2d/498a056cfcef0ec4b0c77e469a946d6b622d92e3b50bc21d799d5dc173b7/scipion_em_tomo3d-3.1.3-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "c3b9caa468dab576021ee73907b2fefc314818a02a8dc7d7c29c46f88812eb2b",
"md5": "7d60dc092fe2044a710ce1f560dcaecf",
"sha256": "3c31ba03c23679e225ff9e514ed9582dd5c8566d441f92bd0da920254baac750"
},
"downloads": -1,
"filename": "scipion-em-tomo3d-3.1.3.tar.gz",
"has_sig": false,
"md5_digest": "7d60dc092fe2044a710ce1f560dcaecf",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 31586,
"upload_time": "2024-10-03T13:26:16",
"upload_time_iso_8601": "2024-10-03T13:26:16.124052Z",
"url": "https://files.pythonhosted.org/packages/c3/b9/caa468dab576021ee73907b2fefc314818a02a8dc7d7c29c46f88812eb2b/scipion-em-tomo3d-3.1.3.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-10-03 13:26:16",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "scipion-em",
"github_project": "scipion-em-tomo3d",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [],
"lcname": "scipion-em-tomo3d"
}
JSON
