========================
Scipion plugin for PySeg
========================
.. image:: https://img.shields.io/pypi/v/scipion-em-pyseg.svg
:target: https://pypi.python.org/pypi/scipion-em-pyseg
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-pyseg.svg
:target: https://pypi.python.org/pypi/scipion-em-pyseg
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-pyseg.svg
:target: https://pypi.python.org/pypi/scipion-em-pyseg
:alt: Supported Python versions
.. image:: https://img.shields.io/pypi/dm/scipion-em-pyseg
:target: https://pypi.python.org/pypi/scipion-em-pyseg
:alt: Downloads
This plugin allows to use PySeg_ - De novo analysis for cryo-electron tomography - within the Scipion framework.
=====
Setup
=====
**System pre-requisites:**
1. Cmake 2.6.3+. The intallation command in Ubuntu is:
.. code-block::
sudo apt-get install cmake
2. GSL (GNU Scientific Library). In Ubuntu, the installation command is:
.. code-block::
sudo apt-get install libgsl-dev
3. gcc/g++ version greater or equal to 5 (for DisPerSE_ compilation).
============
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-pyseg
**2. Developer (latest, may be unstable) version:**:
* Clone the source code repository:
.. code-block::
git clone https://github.com/scipion-em/scipion-em-pyseg.git
* Install:
.. code-block::
scipion3 installp -p local/path/to/scipion-em-pyseg --devel
=========
Protocols
=========
The integrated protocols are:
1. pyseg - fils: Filters a MbGraphMCF (Mean Cumulative Function) object by extracting a filament network
2. pyseg - graphs: Analyzes a GraphMCF (Mean Cumulative Function) from a segmented membrane
3. pyseg - picking: Extracts particles from a filament network of a oriented single membrane graph
4. pyseg - 2D classification: Unsupervised and deterministic classification of membrane-bound particles
5. pyseg - posrec: post-process already reconstructed particles; rot angle randomization and membrane suppression
6. pyseg - preseg membranes: Segment membranes into membranes, inner surroundings and outer surroundings
=====
Tests
=====
The installation can be checked out running some tests (Important: TestPosRec requires the plugins scipion-em-xmipp_
and scipion-em-reliontomo_ to be installed:
.. code-block::
scipion3 tests pyseg.tests.test_preseg_graphs_fils_picking.TestFromPresegToPicking
.. code-block::
scipion3 tests pyseg.tests.test_pos_rec.TestPostRec
========
Tutorial
========
A tutorial about how to use PySeg within Scipion can be found here_.
==========
References
==========
* `Template-free detection and classification of heterogeneous membrane-bound complexes in cryo-electron tomograms. <http://doi.org/10.1038/s41592-019-0675-5>`_
A. Martinez-Sanchez et al., Nature Methods, 2020.
===================
Contact information
===================
If you experiment any problem, please contact us here: scipion-users@lists.sourceforge.net or open an issue_.
We'll be pleased to help.
*Scipion Team*
.. _PySeg: https://github.com/anmartinezs/pyseg_system
.. _DisPerSE: http://www2.iap.fr/users/sousbie/web/html/indexd41d.html
.. _scipion-em-xmipp: https://github.com/I2PC/scipion-em-xmipp
.. _scipion-em-reliontomo: https://github.com/scipion-em/scipion-em-reliontomo
.. _issue: https://github.com/scipion-em/scipion-em-pyseg/issues
.. _here: https://scipion-em.github.io/docs/release-3.0.0/docs/user/denoising_mbSegmentation_pysegDirPicking/tomosegmemTV-pySeg-workflow.html#tomosegmemtv-pyseg-workflow
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"description": "========================\nScipion plugin for PySeg\n========================\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-pyseg.svg\n :target: https://pypi.python.org/pypi/scipion-em-pyseg\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-pyseg.svg\n :target: https://pypi.python.org/pypi/scipion-em-pyseg\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-pyseg.svg\n :target: https://pypi.python.org/pypi/scipion-em-pyseg\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-pyseg\n :target: https://pypi.python.org/pypi/scipion-em-pyseg\n :alt: Downloads\n\nThis plugin allows to use PySeg_ - De novo analysis for cryo-electron tomography - within the Scipion framework.\n\n=====\nSetup\n=====\n\n**System pre-requisites:**\n\n 1. Cmake 2.6.3+. The intallation command in Ubuntu is:\n\n .. code-block::\n\n sudo apt-get install cmake\n\n 2. GSL (GNU Scientific Library). In Ubuntu, the installation command is:\n\n .. code-block::\n\n sudo apt-get install libgsl-dev\n\n 3. gcc/g++ version greater or equal to 5 (for DisPerSE_ compilation).\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-pyseg\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-pyseg.git\n\n* Install:\n\n.. code-block::\n\n scipion3 installp -p local/path/to/scipion-em-pyseg --devel\n\n=========\nProtocols\n=========\nThe integrated protocols are:\n\n1. pyseg - fils: Filters a MbGraphMCF (Mean Cumulative Function) object by extracting a filament network\n\n2. pyseg - graphs: Analyzes a GraphMCF (Mean Cumulative Function) from a segmented membrane\n\n3. pyseg - picking: Extracts particles from a filament network of a oriented single membrane graph\n\n4. pyseg - 2D classification: Unsupervised and deterministic classification of membrane-bound particles\n\n5. pyseg - posrec: post-process already reconstructed particles; rot angle randomization and membrane suppression\n\n6. pyseg - preseg membranes: Segment membranes into membranes, inner surroundings and outer surroundings\n\n=====\nTests\n=====\n\nThe installation can be checked out running some tests (Important: TestPosRec requires the plugins scipion-em-xmipp_\nand scipion-em-reliontomo_ to be installed:\n\n.. code-block::\n\n scipion3 tests pyseg.tests.test_preseg_graphs_fils_picking.TestFromPresegToPicking\n\n.. code-block::\n\n scipion3 tests pyseg.tests.test_pos_rec.TestPostRec\n\n========\nTutorial\n========\nA tutorial about how to use PySeg within Scipion can be found here_.\n\n==========\nReferences\n==========\n\n* `Template-free detection and classification of heterogeneous membrane-bound complexes in cryo-electron tomograms. <http://doi.org/10.1038/s41592-019-0675-5>`_\n A. Martinez-Sanchez et al., Nature Methods, 2020.\n\n===================\nContact information\n===================\n\nIf you experiment any problem, please contact us here: scipion-users@lists.sourceforge.net or open an issue_.\n\nWe'll be pleased to help.\n\n*Scipion Team*\n\n\n.. _PySeg: https://github.com/anmartinezs/pyseg_system\n.. _DisPerSE: http://www2.iap.fr/users/sousbie/web/html/indexd41d.html\n.. _scipion-em-xmipp: https://github.com/I2PC/scipion-em-xmipp\n.. _scipion-em-reliontomo: https://github.com/scipion-em/scipion-em-reliontomo\n.. _issue: https://github.com/scipion-em/scipion-em-pyseg/issues\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\n\n",
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