STracking

STracking is a python framework to develop particles tracking pipeline. This library has been developed to track intra-cellular object in microscopy 2D+t and 3D+t images, but can be use to any spots tracking application in 2D+t and 3D+t images.

System Requirements

Software Requirements

OS Requirements

The STracking development version is tested on Windows 10, MacOS and Linux operating systems. The developmental version of the package has been tested on the following systems:

• Linux: 20.04.4
• Mac OSX: Mac OS Catalina 10.15.7
• Windows: 10

install

Library installation from PyPI

1. Install an Anaconda distribution of Python -- Choose Python 3.9 and your operating system. Note you might need to use an anaconda prompt if you did not add anaconda to the path.
2. Open an anaconda prompt / command prompt with conda for python 3 in the path
3. Create a new environment with conda create --name stracking python=3.9.
4. To activate this new environment, run conda activate stracking
5. To install the STrackinglibrary, run python -m pip install stracking.

if you need to update to a new release, use:

python -m pip install stracking --upgrade

Library installation from source

This install is for developers or people who want the last features in the main branch.

1. Install an Anaconda distribution of Python -- Choose Python 3.9 and your operating system. Note you might need to use an anaconda prompt if you did not add anaconda to the path.
2. Open an anaconda prompt / command prompt with conda for python 3 in the path
3. Create a new environment with conda create --name stracking python=3.9.
4. To activate this new environment, run conda activate stracking
5. Pull the source code from git with `git pull https://github.com/sylvainprigent/stracking.git
6. Then install the STracking library from you local dir with: python -m pip install -e ./stracking.

Use STracking with napari

The STracking library is embedded in a napari plugin that allows using STracking with a graphical interface. Please refer to the STracking napari plugin documentation to install and use it.

STracking documentation

The full documentation with tutorial and docstring is available here