Installation

Track Analyzer installation

with conda

  • If you haven’t installed Python yet, install Python 3.7: download miniconda 3.7: https://docs.conda.io/en/latest/miniconda.html

  • Open a Terminal (Mac & Linux) or open an Anaconda powershell (Windows)

  • Create environment: run conda create -n pyTA python=3.7

  • Activate environment (to be run every time you open a new terminal): run conda activate pyTA

To install Track Analyzer, just run

pip install track-analyzer

with a virtualenv

you can also use a virtual environment.

python3 -m venv pyTA
cd pyTA
source bin/activate
pip install track-analyzer

to exit from the virtualenv

deactivate

To run track-analyzer

cd pyTA
source bin/activate

Archive overview

  • doc => the documentation in html and pdf

  • example => synthetic data examples are stored in the example folder. Each example contains a params.csv file containing for each track the “true” values.

  • track_analyzer => the track analyzer python library

  • setup.py => the installation script

  • requirements.txt => the python dependencies

  • COPYING => the licensing

  • README.md => brief overview

  • run_TA.ipynb => the jupyter notebook used for the graphical interface

Track Analyzer dependencies

Track Analyzer depends on several python packages that will be installed with the pip install:

  • numpy

  • matplotlib

  • pandas

  • scipy

  • scikit-image

  • seaborn

  • jupyter

  • joblib

  • lmfit

  • tifffile

  • napari

  • ipyfilechooser

  • ipywidgets