Apr 28, 2025
Post-Xenium H&E staining and imaging protocol
- Joanna Bi1,
- Chenchen Zhu1,
- Thomas Karathanos1,
- Rongduo Han1
- 1Stanford University
- NCIHTAN
- Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Protocol Citation: Joanna Bi, Chenchen Zhu, Thomas Karathanos, Rongduo Han 2025. Post-Xenium H&E staining and imaging protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.36wgqep6xgk5/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
Created: April 28, 2025
Last Modified: April 28, 2025
Protocol Integer ID: 189166
Abstract
We describe the process we followed for H&E imaging following the Xenium Spatial Transcriptomics assay.
Staining
Staining
10x_CG000613_Demonstrated_Protocol_Xenium_H_EStaining_RevB.pdf2MB We used the guide provided by 10x Genomics for staining following a Xenium assay. Link: https://cdn.10xgenomics.com/image/upload/v1704391942/support-documents/10x_CG000613_Demonstrated_Protocol_Xenium_H_EStaining_RevB.pdfImaging
Imaging
After coverslipping and drying, image slides at 40X in brightfield.
Pre-processing
Pre-processing
parse_ndpi.py2KB After the images are captured, split images from TMA using imaging software or code. We used a Python script to split serial sections of each .ndpi image corresponding to different slides. Sample code is attached.