Toolset for single-cell trajectory modeling.


License
MIT
Install
pip install celltraj==0.1.52

Documentation

celltraj

A toolset for the modeling and analysis of single-cell trajectories.

Key Features

  • Single-Cell Trajectory Analysis: Leverages time-lapse imaging data to construct detailed trajectories of single-cell behavior, capturing changes in morphology and motility.
  • Morphodynamical State Decomposition: Utilizes data-driven methods to define and analyze cell states based on dynamic cellular features, providing insights into cell state transitions.
  • Dynamical Modeling: Implements MSMs and Koopman operator-based approaches to kinetically characterize cell state transitions and generate embeddings for visualizing cell dynamics.
  • Integration with Molecular Data: Maps live-cell imaging data to gene expression profiles, enabling predictions of RNA transcript levels based on cell state dynamics.
  • Tutorials: Includes jupyter-notebooks with links to Zenodo repositories with downloadable data to guide users through the process of trajectory embedding and MMIST (Molecular and Morphodynamics-Integrated Single-cell Trajectories).

References

  • Copperman, Jeremy, Sean M. Gross, Young Hwan Chang, Laura M. Heiser, and Daniel M. Zuckerman. “Morphodynamical cell state description via live-cell imaging trajectory embedding.” Communications Biology 6, no. 1 (2023): 484.
  • Copperman, Jeremy, Ian C. Mclean, Sean M. Gross, Young Hwan Chang, Daniel M. Zuckerman, and Laura M. Heiser. “Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change.” bioRxiv (2024): 2024-01.

License

Free software: MIT license

Documentation

Tutorials

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.