Susan Glenn

Topological data analysis (TDA) uses persistent homology to quantify loops and higher-dimensional holes in data, making it particularly relevant for examining the characteristics of images of cells in the field of cell biology. In the context of a cell injury, as time progresses, a wound in the form of a ring emerges in the cell image and then gradually vanishes. Performing statistical inference on this ring-like pattern in a single image is challenging due to the absence of repeated samples. In this paper, we develop a novel framework leveraging TDA to estimate underlying structures within an individual image and quantify associated uncertainties through confidence regions. Our proposed method partitions the image into the background and the damaged cell regions. Then, pixels within the affected cell region are used to establish confidence regions in the space of persistence diagrams (topological summary statistics). The proposed method establishes an estimate of a persistence diagram for an image that mitigates the bias of a traditional persistence diagram computation. A simulation study is conducted to evaluate the coverage probabilities of the proposed confidence regions in comparison to an alternative approach that is proposed in this paper. We also illustrate our methodology by a real-world example provided by biological cell repair.

Topological Data Analysis (TDA) can be used to detect and characterize holes in an image, such as zero-dimensional holes (connected components) or one-dimensional holes (loops). However, there is currently no widely accepted statistical framework for modeling spatiotemporal dependence in the evolution of topological features, such as holes, within a time series of images. We propose a hypothesis testing framework to identify statistically significant topological features of images in space and time, simultaneously. This addition of time may induce higher-dimensional topological features which can be used to establish temporal connections between the lower-dimensional features at each point in time. The temporal evolution of these lower-dimensional features is then represented on a zigzag persistence diagram, as a topological summary statistic focused on time dynamics. We demonstrate that the method effectively captures the emergence and progression of topological features in a study of a series of images of a wounded cell as it repairs. The proposed method outperforms a current approach in a simulation study that includes features of the wound healing process. Since, the wounded cell images exhibit nonlinear, dynamic, spatial, and temporal structures during single-cell repair, they provide a good application for this method.