stracking 0.1.5

Implementation of particle tracking algorithms for 2D+t and 3D+t scientific data

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.

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