Pyto

General description

Detection and analysis of macromolecular complexes and proteins in 3D cryo-electron images (tomograms). While it was developed for neuronal synapses, it is applicable to other biological systems.

Specific tasks

• The main purpose is the detection and analysis of pleomorphic membrane-bound molecular complexes cryo-electron tomograms.

• Correlate images obtained from light microscopy and different modes of electron microscopy (transmission and scanning electron microscopy, focused ion beam microscopy). A part of this code is used in 3DCT package for correlative microscopy, which provides GUI.

• Spatial distribution analysis of particles (such as complexes)

• Preprocessing membrane-bound particles (complexes) for subtomogram averaging.

• Mapping complexes to their exact position and angular orientation for visualization.

• Provides tools that assist general processing of cryo-electron tomograms (frame alignment, 3D reconstruction).

Dependencies:

The current version is written in Python 3. The code was originally written in Python 2 and subsequently converted to Python 3.6. While most of the code is currently compatible with Python 2.7, this will not be enforced in future.

The major dependencies of this package are:

• NumPy

• SciPy
• Pandas
• future

In addition, some parts depend on:

• Matplotlib
• Sklearn
• Skimage
• Statsmodels
• SymPy: Currently needed only for development
• PySeg: Needed only if Pyseg colocalization processing is followed by Pyto. Make sure Pyto comes before PySeg in PYTHONPATH because PySeg contains an older version of Pyto

Installation

Put this directory to your PYTHONPATH

Documentation

Please start from Overview.

Release history

• 1.10.2 (30.03.2025, svn r2181)
  • Added mapping particle code and example
  • Fixed some depreciation related issues for python 3.12
  • Docs improvements, small fixes
• 1.10.1 (07.01.2025, svn r2155)
  • Added preprocessing for subtomo averaging example
  • Put back sources for manuals
• 1.10.0 (18.12.2024, svn r2140)
  • Added preprocessing for subtomo averaging
  • Improved particle handling (MultiParticlesets)
  • The above are needed for the Tether averaging project
• 1.9.2 (19.03.2024, svn r2102)
  • Added projection methods for colocalization analysis
  • Added particle extraction from tomos
  • Removed dependence on imp module to make pyseg compatible with Python 3.12+
• 1.9.1 (18.10.2023, svn r2024)
  • Noted future module dependency
  • Removed references to numpy.testing.Tester (removd from numpy 1.24)
• 1.9 (7.12.2021, svn r1824)
  • Added colocalization analysis (developed for Martinez-Sanchez et al 2021 "Trans-synaptic assemblies link synaptic vesicles and neuroreceptors" DOI: 10.1126/sciadv.abe6204)
  • Added functionality to extract additional features of segments
• 1.8 (31.10.2021, svn r1771)
  • Added classes for basic geometrical shapes (Plane, Parallelogram)
  • Added bin_crop script
  • Improved analysis: Groups to/from Pandas, correlation analysis and graphs
• 1.7
  • Added presynaptic example
  • Improved docs
  • Small improvements
• 1.6
  • The first public release.

License

Copyright (C) 2010 Vladan Lucic

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

Citing

Please consider citing us if you use Pyto:

• For general use, segmentation and analysis: Lučić V, Fernández-Busnadiego R, Laugks U and Baumeister W, 2016. Hierarchical detection and analysis of macromolecular complexes in cryo-electron tomograms using Pyto software. J Struct Biol. 196(3):503-514. http://dx.doi.org/10.1016/j.jsb.2016.10.004.

• For 3D to 2D correlation, please cite: Arnold, J., J. Mahamid, V. Lucic, A. d. Marco, J.-J. Fernandez, Laugks, H.-A. Mayer, Tobias, W. Baumeister, and J. Plitzko, 2016. Site-specific cryo-focused ion beam sample preparation guided by 3-dimensional correlative microscopy. Biophysical Journal 110:860-869. http://dx.doi.org/10.1016/j.bpj.2015.10.053.

• For all other correlative work: Fukuda, Y., N. Schrod, M. Schaffer, L. R. Feng, W. Baumeister, and V. Lucic, 2014. Coordinate transformation based cryo-correlative methods for electron tomography and focused ion beam milling. Ultramicroscopy 143:15– 23. http://dx.doi.org/10.1016/j.ultramic.2013.11.008.

Thank you.

Author

Vladan Lucic (vladan@biochem.mpg.de), Max Planck Institute for Biochemistry