Abstract
Recently, high-throughput spatial transcriptomics (HST) technologies (e.g., 10X Genomics Visium, Slide-seq,
and Slide-seqV2) have made it possible to simultaneously measure close-to-cell-level gene expressions and
spatial locations of these cells within a tissue or organ. These new technologies have provided an unprecedented
opportunity to investigate cellular heterogeneity and cell-cell communications. Although a few computational
tools for HST data analysis have recently become available, a rigorous statistical framework for design of HST
experiments is still missing in the literature. Researchers planning an HST experiment need to determine various
experimental design parameters such as the sequencing depth, and these choices affect whether key goals of
HST experiments can be achieved, e.g., identification of tissue architecture, spatially variable genes, and cell-
cell communications. In this proposal, we aim to develop a rigorous power analysis framework for HST
experiments. The assembled team has strong and complementary expertise in statistical modeling of HST data,
development of statistical frameworks and software for power analysis and design of high throughput sequencing
data, single-cell genomics technologies, spatial statistics, computational tool development, and utilization of
these computational tools for investigation of molecular and immunologic basis of diseases. We will achieve the
proposed goal by implementing two specific aims. In Aim 1, we will develop a rigorous power analysis framework
for HST experiments. In Aim 2, we will develop an interactive web interface and an R package for power analysis
of HST experiments. The proposed power analysis framework will be developed and evaluated using simulation
data, HST data in the public domain, and in-house HST datasets from collaborators. The statistical framework
that will be developed in this project, along with the open-source software implementing this framework, will
provide essential tools for the optimal design of future HST experiments.