Question: How does Xenium perform cell segmentation?
Answer: Xenium includes a cell segmentation step as part of onboard analysis. The cell segmentation steps differ depending on whether the run is RNA-only or adds Multimodal Cell Segmentation. See the official Support site documentation for the most up-to-date algorithm details at https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/algorithms-overview/segmentation.
Other Resources:
- Xenium Nature publication: High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis
- Analysis Guides article: Performing 3D Nucleus Segmentation With Cellpose and Generating a Feature-cell Matrix
- Analysis Guides article: Using Baysor to Perform Xenium Cell Segmentation
Products: Xenium In Situ Gene Expression
Last update: March 27, 2024