TrackPal: Tracking Python AnaLyzer

A modular library for the analysis of object trackings in Python with pandas.

Overview

Main features

• Read Imaris / TrackMate files
• Simulate tracks with different motion types
• Compute track feature descriptors (~50 available features)
• Mean squared displacement curves for single tracks and ensembles
• Velocity autocorrelation curves for single tracks and ensembles
• Visualization utilities

For most computations TrackPal relies on pandas groupby and apply mechanism.

TrackPal does not track or link objects. It analyzes already tracked objects. For obtaining object trackings from images or detections see for instance the excellent projects TrackMate, trackpy or ilastik

Examples

Simple simulation and plotting

import trackpal as tp

trj = tp.simulate.brownian_linear(n_tracks=10)

trj.groupby("TrackID").apply(
    tp.visu.plot_trj, coords=["Position X", "Position Y"], line_fmt=".-",
)

Output:

Track features

• Simulate different motion types and compute track feautures
  • Features

Mean squared displacement curves

• Calculate diffusion constant and velocity from different simulated motion types
  • MSD

Installation

Anaconda Python (>=3.6) and a new environment are recommended

0. Install Anaconda Python (>=3.6)

conda create --name trackpal_env --python=3.7
conda activate trackpal_env

Dependencies

• numpy
• pandas
• scikit_image
• scikit_learn
• tifffile
• tqdm
• scipy
• statsmodels
• matplotlib
• rdp
• tqdm

From PyPi:

1. pip install TrackPal

For development

1. git clone this repository
2. cd trackpal
3. pip install -e .

Documentation

• GitHub mirror
• GitLab IST
• API documentation