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