Welcome to TRAIT2D’s documentation!

TRAIT2D (available as trait2d) is a cross-platform Python software package with compilable graphical user interfaces (GUIs) to support Single Particle Tracking (SPT) experiments.

Features

• SPT simulation, tracking and analysis
• user-friendly GUIs for simple tasks
• customisable libraries for more advanced users
• open source under the GNU General Public License

Installation

Installation methods have been tested on Linux and Windows.

Install from PyPI (Recommended)

Prerequisites:

• A Python installation (version >= 3.7 is required)

Installation:

• run pip install trait2d

Install from Source (Not Recommended)

Prerequisites:

• A Python installation (version >= 3.7 is required)
• Optional: A Git installation

Installation:

• clone the GitHub repository

  • run git clone https://github.com/Eggeling-Lab-Microscope-Software/TRAIT2D

  • OR

    • visit https://github.com/Eggeling-Lab-Microscope-Software/TRAIT2D
    • click the green Code button and then Download ZIP
    • extract the downloaded .zip file anywhere on your computer

• change to the directory that was just created (should contain a setup.py file)

• run pip install -e .

Libraries

• Analysis Library
  • Analysis Methods
  • Single Track
  • Multiple Tracks
  • ModelDB
  • Models
• Simulation Library
• Exceptions

Graphical Applications

• Analysis GUI
  • Starting the GUI
  • Description of the GUI
• Simulator GUI
  • Starting the GUI
  • Description of the GUI
• Tracker GUI
  • Starting the GUI
  • Description of the GUI

File Formats

• CSV Files
  • Data Structure
  • Units

Tutorials and Examples

• Example gallery

Project Maintenance

• Project Maintenance
  • Releasing on PyPI

Indices and tables

• Index
• Module Index
• Search Page

Dependencies

The trait2d package depends on external libraries. If you followed the instructions in the Installation section, these should be installed automatically.

They are nevertheless listed here for completeness:

Package Name	License
imageio	BSD License (BSD-2-Clause)
matplotlib	Python Software Foundation License (PSF)
numpy	OSI Approved (BSD)
opencv-python	MIT License (MIT)
pandas	BSD
pyqtgraph	MIT License (MIT)
PyQt5	GPL v3
scikit-image	BSD License (Modified BSD)
scipy	BSD License (BSD)
tk	Apache Software License (Apache 2.0 Licence)
tqdm	MIT License, Mozilla Public License 2.0 (MPL 2.0) (MPLv2.0, MIT Licences)