# Defining Keypoints to Align H&E Images and Xenium DAPI-Stained Images Automatically

## TL;DR

Xenium-Align is a new method that automatically aligns H&E and Xenium images, reducing the need for manual work in spatial transcriptomics studies.

## Contribution

Xenium-Align introduces an automated keypoint identification method for aligning H&E and Xenium images.

## Key findings

- Xenium-Align was validated on 14 human kidney and one human skin sample with expert results.
- The method generated accurate keypoints for image alignment in Xenium Explorer software.
- Future work focuses on improving runtime efficiency and usability.

## Abstract

10X Xenium is an in situ spatial transcriptomics platform that enables single-cell and subcellular-level gene expression analysis. In Xenium data analysis, defining matched keypoints to align H&E and spatial transcriptomic images is critical for cross-referencing sequencing and histology. Currently, it is labor-intensive for domain experts to manually place keypoints to perform image registration in the Xenium Explorer software. We present Xenium-Align, a keypoint identification method that automatically generates keypoint files for image registration in Xenium Explorer. We validated our proposed method on 14 human kidney samples and one human skin Xenium sample representing healthy and diseased states, with expert manually marked results. These results show that Xenium-Align could generate accurate keypoints for automatically implementing image alignment in the Xenium Explorer software for spatial transcriptomics studies. Our future research aims to optimize the method’s runtime efficiency and usability for image alignment applications.