mauva27/particle_tracking

Code for tracking of particles

Particle Tracking

Package that performs tracking of colloidal particles in 2D. Based on conventional tracking methods used in this paper. This is version based on a tracking code written in R (see Repo). NOTE: other available packages, such as Trackpy, allow particle tracking in 2D & 3D.

Installation

Use

pip install particle-tracking

to simply install the code.

Using the code

the simples way to run the code is busing a jupyer notebook. See templates inside particle_tracking/example/. Start with

import particle_tracking as pt

The code has three main class objects Tracker, Linker & Filtering, which allow to detect particles, reconstruct individual trajectories (using Trackpy's linking method, and filter trajectories respectively. Simply use

pt.Tracker()
pt.Linker()
pt.Filtering

to access the main functions. NOTE: all of the class obejct above require params, a dictionary containing parameters to exceute the tracking methods. See the next section to learn how to generate params.

Interactive Menu

The code includes an interactive widget that allows to select and modify quickly the input parameters. Import the interactive menu using

from particle_tracking.src  import menus
menu = menus.MainMenu()
menu.options

Once the parameters are selected use

params = menus.return_params(menu.options.children)

Characterisation

The code includes extra tools to characterise the samples onced they have been tracked. Structural order and dynamics can be anylsed by means of $\psi_{6}$ and mean-squared displacements. For example,

from particle_tracking.src.characterisation import Psi6
psi6 = Psi6()

or

from particle_tracking.src.characterisation import MSD
msd = MSD()