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Open Source Research Software

  • Built in Python using packages from the Scientific Python and data science ecosystem

  • Packaged into submodules with a Jupyter Notebook interface

  • Documented, version-controlled; built to be understood and re-used

Example project: 

cell PLasticity Analysis TOol  (cellPLATO):

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cellPLATO: an unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data

Michael J. Shannon, Shira E. Eisman, Alan R. Lowe, Tyler Sloan, Emily M. Mace

doi: https://doi.org/10.1242/jcs.261887

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A data-processing, analysis, and visualization pipeline for single-cell time-lapse data.


Features:

  • Pooling and comparing replicate experiments from multiple conditions.

  • Shape measurements via SciKit-Image

  • Accepts cell-tracking result input from Bayesian Tracker or Usiigaci. 

  • Dimensionality Reduction

  • Systematic plot output for user-specified factors

  • User-friendly Jupyter Notebook interface to interact with modular Python package

  • Version controlled Open Source Research Software, see the project hosted on Github.

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