Pyto

Description

The main purpose of Pyto package is to provide tools for the detection and analysis of pleomorphic membrane-bound molecular complexes in 3D images (tomograms). It is designed for cryo-electron tomograms of neuronal synapses, but it can be used for other biological systems.

In addition, Pyto can be used to 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.

Finaly, tools that assist general processing of cryo-electron tomograms (frame alignment, 3D reconstruction) are also provided.

Dependencies:

The current version is written in Python 3. The code was originally written in Pythin 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

In addition, some parts depend on:

• Matplotlib
• Pandas

Installation

Put this directory to your PYTHONPATH

Documentation

Please start from Overview.

Release history

• 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