A modular library for the analysis of object trackings in Python with pandas.
- 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
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=".-",
)
- Simulate different motion types and compute track feautures
- Calculate diffusion constant and velocity from different simulated motion types
Anaconda Python (>=3.6) and a new environment are recommended
- Install Anaconda Python (>=3.6)
conda create --name trackpal_env --python=3.7
conda activate trackpal_env
- numpy
- pandas
- scikit_image
- scikit_learn
- tifffile
- tqdm
- scipy
- statsmodels
- matplotlib
- rdp
- tqdm
pip install TrackPal
git clone
this repositorycd trackpal
pip install -e .