u-Unwrap3D Analysis Notebooks#
This collection of Python jupyter notebooks are written for Python users who are interested in analyzing three dimensional cell surfaces, particularly interrogating the co-fluctuation of surface morphology with other surface-associated measurements which may be but not limited to: activity of molecular markers, cell-cell interactions, cell-environment interactions etc. It uses the u-Unwrap3D package which is described in the following technical papers:
u-Unwrap3D: Surface-guided computing to analyze subcellular morphology and membrane-associated signals in 3D
Structure of this book#
The book will first cover installation and implement the standard pipeline for performing the main analytical steps of transforming an input 3D surface and 3D image into lower-dimensional representations for analysis first described in publication 1 above. Then specific chapters are dedicated to provide more detailed explanations of the algorithms used, and how to customize and extend the standard workflow to timelapse image analysis.
The notebooks aim to be self-contained, self-explanatory and fully reproducible. Hence, the reader can download this Jupyter book and execute all notebooks as they are.
As a general requirement, a separate conda environment should be initialized on the reader’s computer as explained in the first chapter.