Scipion plugin for PySeg
This plugin allows to use PySeg - De novo analysis for cryo-electron tomography - within the Scipion framework.
Setup
System pre-requisites:
- Cmake 2.6.3+. The intallation command in Ubuntu is:
sudo apt-get install cmake
- GSL (GNU Scientific Library). In Ubuntu, the installation command is:
sudo apt-get install libgsl-dev
- 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::
scipion3 installp -p scipion-em-pyseg
2. Developer (latest, may be unstable) version::
- Clone the source code repository:
git clone https://github.com/scipion-em/scipion-em-pyseg.git
- Install:
scipion3 installp -p local/path/to/scipion-em-pyseg --devel
Protocols
The integrated protocols are:
- pyseg - fils: Filters a MbGraphMCF (Mean Cumulative Function) object by extracting a filament network
- pyseg - graphs: Analyzes a GraphMCF (Mean Cumulative Function) from a segmented membrane
- pyseg - picking: Extracts particles from a filament network of a oriented single membrane graph
- pyseg - 2D classification: Unsupervised and deterministic classification of membrane-bound particles
- pyseg - posrec: post-process already reconstructed particles; rot angle randomization and membrane suppression
- 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:
scipion3 tests pyseg.tests.test_preseg_graphs_fils_picking.TestFromPresegToPicking
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. 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
