tramway

TRamWAy

The TRamWAy library features various tools for the analysis of particle dynamics in Single Molecule Localization Microscopy (SMLM) data. It can resolve the diffusivity, drift, force and potential energy in space and time.

The original documentation is now on readthedocs.

An attempt to rewrite the project documentation is available as a separate project and web resource.

Installation

You will need Python >= 3.6.

Windows users

Please favor Conda, as Conda will seamlessly install the HDF5 standard library which is a required dependency.

From PyPI

pip install tramway

pip install will install some Python dependencies if missing, but you may still need to install the HDF5 reference library.

Note that the HDF5 library can usually be installed using any OS' package manager. Only Windows users may have to manually download and install the HDF5 library, if they do not wish to use Conda instead of pip.

Several installation targets are available, including full, that install optional dependencies:

pip install tramway[full]

Most of the functionalities and code examples described in the documentation will run without optional dependencies. It is safe to first install TRamWAy with minimal requirements and then pip install the missing dependencies as you hit ImportError while using TRamWAy.

Using Conda

conda install tramway -c conda-forge

Compared with the bare package pip installs (with no installation targets), the conda package specifies some optional dependencies as required, so that the above command installs them. However, many other optional dependencies are omitted.