[moved] How to align image to cropped data, visualize with Xenium Explorer

Moved from GitHub Coordinates from Xenium Explorer not matching the original data · Issue #167 · scverse/spatialdata-io · GitHub, originally asked from Yifan-debug (yifan wang) · GitHub.

Original question: in my case, I only focus on a small region of the whole slide. So I only take high-resolution confocal images specifically of this small region after Xenium. I’m wondering if there is any tutorial I could follow not only for cropping the image but also for aligning my confocal image to the cropped image and outputting a folder that the locations of transcripts can be visualized in Xenium Explorer.

Here is the answer.
We don’t have a tutorial for what you asked exactly, but the various compoents to achieve this are explained in some other tutorials.

Hope this leads to the solution, let me know if you have any other question.