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:

1. Cmake 2.6.3+. The intallation command in Ubuntu is:

sudo apt-get install cmake

2. GSL (GNU Scientific Library). In Ubuntu, the installation command is:

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::

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:

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:

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