A toolbox to analyze lymphocyte tracks within lymphnodes from microscopy or simulations. It is based on Pandas, numpy, matplotlib, seaborn, statsmodels, scikit-learn and scikit-image and produces figures like the following motility analysis:
- motility.py: Tools to analyze cell motility from positions within lymph nodes.
- remix.py: Statistical models to generate tracks based on data.
- contacts.py: Simulate contacts between T cells and dendritic cells.
- imaris.py: Loads cell tracks from excel spreadsheets exported from Imaris.
- volocity.py: Loads Volocity cell tracks.
- spim.py: Displays and finds cells in SPIM (Single Plane Illumination Microscopy) data.
To install the required packages run $ pip install -r requirements.txt. For usage see the examples in if __name__ == '__main__' in the corresponding module.py, which can be executed with $ python -m lana.module.