u-Unwrap 0.1.0

Map 2D cellular shapes to disk, square and rectangle representations for analysis

u-unwrap2D

Library for 2D Contour-guided computing

August 29, 2024

u-Unwrap2D is a Python library built on top of u-Unwrap3D to map 2D contours and images into canonical representations to facilitate analysis with particular attention to single cell biology.

u-Unwrap2D or u-Unwrap is associated with the manuscript: Mapping Cell Morphology to a Standard Coordinate System for Analyzing Dynamic Cell Signaling, Imageomics NeurIPS Workshop, 2025, written by Shiqiu Yu, Gaudenz Danuser, Felix Y. Zhou.

The functions in this library on built on the idealogy of u-Unwrap3D for 2D. For more information please read: Surface-guided computing to quantify dynamic interactions between cell morphology and molecular signals in 3D, bioRxiv, 2025, written by Felix Y. Zhou, Virangika K. Wimalasena, Qiongjing Zou, Andrew Weems, Gabriel M. Gihana, Edward Jenkins, Bingying Chen, Bo-Jui Chang, Meghan K. Driscoll, Andrew J. Ewald and Gaudenz Danuser.

Library Features

Module	Functionality
unwrap2D	Functions for unwrapping 2D contours and mapping images to disk and square representations. Much recycle/adapt u-Unwrap3D functions.

Getting Started

The simplest way to get started is to check out the included notebooks which walks through the steps described in the paper for obtaining all representation starting from step0: the extraction of surface from a binary cell segmentation.

Dependencies and Installation

You should be able to install the library using pip:

pip install .

Should this fail, the only dependency is u-Unwrap3D, our 3D unwrapping library which can be installed using the command below from PyPI or from its GitHub, https://github.com/DanuserLab/u-unwrap3D. u-Unwrap3D has been tested for Python 3.9-3.12. You can try installing that library first, then perform the above pip install ..

pip install u-Unwrap3D

Questions and Issues

Feel free to open a GitHub issue, and we will get back as soon as we can.

Developers

Felix Zhou ([e-mail])

Shiqiu Yu ([e-mail])

Danuser Lab Links

Danuser Lab Website

Software Links