pyseg_system (v 2.0.0)

De novo analysis for cryo-electron tomography.

This GitHub repository have two branches (git checkout <feature_branch>):

• master: (default) stable Python 3 version.
• python2: old Python 2.7 (deprecated).
• python3: branch with the latest modifications and improved.

What's new from v2.0.1

Python 3 transition completed and changes for being compatible with Scipion. Now PySeg has been ugraded to run Ubunutu 22.04 LTS.

CONTENTS

• data: input data for running some tests and tutorials, output and intermediate data stored here during tutorials and tests execution are cleaned by running clean_out_data.sh.
• code: the code (libraries and execution scripts) for PySeg, PyOrg and TomoSegMemTV.
• sys: third party software with their installers.
  • DisPerSe (v. 0.9.24)
    • Cfitsio (v. 3.380)
  • CGAL (v 4.7)
  • Graph-tool
  • VTK
• doc: documentation files
  • manual: a general manual, with installation instructions included, for PySeg
  • tutorials: specific examples to introduce the users in the usage of the software
    • synth_sumb: basic tutorial for using PySeg for single unoriented membranes using synthetic data
    • synth_ssmb: Deprecated, just for testing.
    • exp_sumb: additional and modified scripts in respect to synth_sumb to process single uoriented membranes from experimental data.
    • exp_somb: additional and modified scripts in respect to synth_sumb to process single oriented membranes from experimental data.
    • exp_domb: additional and modified scripts in respect to synth_sumb to process double oriented membranes from experimental data.
  • tomosegmemtv: documentation for TomoSegMemTV (membrane segmentation for electron tomogramphy)
  • synapsegtools: documentation for SynapSegTools (some graphic extension for post-processing the outputs of TomoSegMemTV)

INSTALLATION

A description of the requirements, auxiliary software, installation and functionality testing is available on docs/manual/manual.pdf file.

BUILDING AND RUNNING WITH DOCKER

You may want to build a docker container to run Pyseg. First, you have build docker image in Dockerfile:

docker build . -t pyseg:latest

Then you can run a terminal on image by:

docker run -it pyseg:latest bash

In this terminal, you can work like in any other Linux terminal having acces to the whole Pyseg funcitionality. If you just want to run a specific script then (replace the <> placeholders accordingly, a typical location for the is /mnt):

docker run --rm -it -v <data-directory-in-host-machine>:<mount-directory-in-container> pyseg:latest <command> <options>

For the available commands look at USAGE.

USAGE

In docs/tutorials/synth_sumb/synth_sumb.pdf there is a tutorial for de novo analysis of membrane proteins using self-generated synthetic data, it is strongly recomended to complete this tutorial before starting with your experimental data.

REPORTING BUGS

If you have found a bug or have an issue with the software, please open an issue here.

LICENSE

Licensed under the Apache License, Version 2.0 (see LICENSE file)

PUBLICATIONS

• Template-free particle picking and unsupervised classification (PySeg):

    [1] Martinez-Sanchez, A., Kochovski, Z., Laugks, U. et al. Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms. Nat Methods 17, 209–216 (2020). https://doi.org/10.1038/s41592-019-0675-5
  

• Membrane segmentation (TomoSegMemTV):

    [2] Martinez-Sanchez et al. "Robust membrane detection based on tensor voting for electron tomography" J Struct Biol (2014) https://doi.org/10.1016/j.jsb.2014.02.015
  

• Statistical spatial analysis (PyOrg):

    [3] Martinez-Sanchez, Lucic & Baumeister. "Statistical spatial analysis for cryo-electron tomography" Comput Methods Programs Biomed (2022) https://doi.org/10.1016/j.cmpb.2022.106693