=====================================================
Scipion plugin for TomoSegMemTV and MembraneAnnotator
=====================================================
.. image:: https://img.shields.io/pypi/v/scipion-em-tomosegmemtv.svg
:target: https://pypi.python.org/pypi/scipion-em-tomosegmemtv
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-tomosegmemtv.svg
:target: https://pypi.python.org/pypi/scipion-em-tomosegmemtv
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-tomosegmemtv.svg
:target: https://pypi.python.org/pypi/scipion-em-tomosegmemtv
:alt: Supported Python versions
.. image:: https://img.shields.io/pypi/dm/scipion-em-tomosegmemtv
:target: https://pypi.python.org/pypi/scipion-em-tomosegmemtv
:alt: Downloads
Scipion plugin for segmentation and annotation of membranes in tomograms (with TomoSegmenTV_ and memb-annotator_,
respectively)
============
Installation
============
The plugin can be installed in user (stable) or developer (latest, may be unstable) mode:
**1. User (stable) version:**:
.. code-block::
scipion3 installp -p scipion-em-tomosegmemtv
**2. Developer (latest, may be unstable) version:**:
* Clone the source code repository:
.. code-block::
git clone https://github.com/scipion-em/scipion-em-tomosegmemtv.git
* Install:
.. code-block::
scipion3 installp -p local/path/to/scipion-em-tomosegmemtv --devel
=========
Protocols
=========
The integrated protocols are:
1. tomosegmemtv - annotate segmented membranes: Manual annotation tool for segmented membranes.
2. tomosegmemtv - resize segmented or annotated volume: Resize segmented volumes or annotated (TomoMasks).
3. tomosegmemtv - tomogram segmentation: segment membranes in tomograms.
=====
Tests
=====
The installation can be checked out running some tests (Important: test_resize_tomomask requires the plugin
scipion-em-imod_ to be installed).
.. code-block::
scipion3 tests tomosegmemtv.tests.test_tomosegmemtv
.. code-block::
scipion3 tests tomosegmemtv.tests.test_resize_tomomask
========
Tutorial
========
A tutorial about how to use tomosegmemtv and the membrane annotator within Scipion can be found here_.
==========
References
==========
* `Robust membrane detection based on tensor voting for electron tomography. <https://doi.org/10.1016/j.jsb.2014.02.015>`_
A. Martinez-Sanchez, I. Garcia, S. Asano, V. Lucic, J.J. Fernandez.
Journal of Structural Biology 186:49-61, 2014.
===================
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*
.. _TomoSegmenTV: https://sites.google.com/site/3demimageprocessing/tomosegmemtv
.. _memb-annotator: https://github.com/anmartinezs/memb-anotator
.. _scipion-em-imod: https://github.com/scipion-em/scipion-em-imod
.. _here: https://scipion-em.github.io/docs/release-3.0.0/docs/user/denoising_mbSegmentation_pysegDirPicking/tomosegmemTV-pySeg-workflow.html#tomosegmemtv-pyseg-workflow
.. _issue: https://github.com/scipion-em/scipion-em-tomosegmemtv/issues
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"description": "=====================================================\nScipion plugin for TomoSegMemTV and MembraneAnnotator\n=====================================================\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-tomosegmemtv.svg\n :target: https://pypi.python.org/pypi/scipion-em-tomosegmemtv\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-tomosegmemtv.svg\n :target: https://pypi.python.org/pypi/scipion-em-tomosegmemtv\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-tomosegmemtv.svg\n :target: https://pypi.python.org/pypi/scipion-em-tomosegmemtv\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-tomosegmemtv\n :target: https://pypi.python.org/pypi/scipion-em-tomosegmemtv\n :alt: Downloads\n\nScipion plugin for segmentation and annotation of membranes in tomograms (with TomoSegmenTV_ and memb-annotator_,\nrespectively)\n\n============\nInstallation\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 scipion3 installp -p scipion-em-tomosegmemtv\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-tomosegmemtv.git\n\n* Install:\n\n.. code-block::\n\n scipion3 installp -p local/path/to/scipion-em-tomosegmemtv --devel\n\n=========\nProtocols\n=========\nThe integrated protocols are:\n\n1. tomosegmemtv - annotate segmented membranes: Manual annotation tool for segmented membranes.\n\n2. tomosegmemtv - resize segmented or annotated volume: Resize segmented volumes or annotated (TomoMasks).\n\n3. tomosegmemtv - tomogram segmentation: segment membranes in tomograms.\n\n=====\nTests\n=====\n\nThe installation can be checked out running some tests (Important: test_resize_tomomask requires the plugin\nscipion-em-imod_ to be installed).\n\n.. code-block::\n\n scipion3 tests tomosegmemtv.tests.test_tomosegmemtv\n\n.. code-block::\n\n scipion3 tests tomosegmemtv.tests.test_resize_tomomask\n\n========\nTutorial\n========\nA tutorial about how to use tomosegmemtv and the membrane annotator within Scipion can be found here_.\n\n==========\nReferences\n==========\n\n* `Robust membrane detection based on tensor voting for electron tomography. <https://doi.org/10.1016/j.jsb.2014.02.015>`_\n\n A. Martinez-Sanchez, I. Garcia, S. Asano, V. Lucic, J.J. Fernandez.\n Journal of Structural Biology 186:49-61, 2014.\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\nan issue_.\n\nWe'll be pleased to help.\n\n*Scipion Team*\n\n\n.. _TomoSegmenTV: https://sites.google.com/site/3demimageprocessing/tomosegmemtv\n.. _memb-annotator: https://github.com/anmartinezs/memb-anotator\n.. _scipion-em-imod: https://github.com/scipion-em/scipion-em-imod\n.. _here: https://scipion-em.github.io/docs/release-3.0.0/docs/user/denoising_mbSegmentation_pysegDirPicking/tomosegmemTV-pySeg-workflow.html#tomosegmemtv-pyseg-workflow\n.. _issue: https://github.com/scipion-em/scipion-em-tomosegmemtv/issues\n\n\n\n",
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