Question: My Xenium sample shows transcripts not captured by cells. How can I rescue the transcripts and assign them to cells?
Answer: For each of the following contexts, we outline different approaches to rescue transcripts outside of cells. This article gathers the multiple contexts.
- Brain fraction of transcripts within cells is low
- Boundary stain shows cell type better than the interior stain
- Other contexts are in the works and will be added as resources become available.
The rescue approach should depend on the downstream analysis goal. Researchers should consider whether the transcript gains are worth the tradeoffs the rescue approach entails. For example, when applying a larger nucleus expansion distance, consider whether capturing more transcripts per cell is worth the increased admixture of different cell type transcripts. Similarly, when disabling boundary or interior stain logic with xeniumranger-v2+, remember Xenium Multimodal Cell Segmentation has higher specificity because cell definitions are based on biological features. Finally, keep in mind all transcripts, whether captured in a cell or not, are recorded in the transcripts result (parquet or zarr.zip) and visualized by Xenium Explorer.
- Multimodal Cell Segmentation is detailed in the technical note here.
- We offer a QC tutorial for Multimodal Cell Segmentation using Xenium Explorer here.
- After following the steps in the tutorial, for any cell type where it is obvious segmentation algorithm performance could be improved, please contact us at support@10xgenomics.com. Attach independent images of the stains and then an image with nucleus and cell outlines overlaid and colored by segmentation method. Include the scale bar. In Xenium Explorer, exporting the PNG using the
button will automatically include the scale bar.
We are continuously improving our segmentation models and these updates will become available to researchers in xeniumranger, so that older data can be analyzed with newer models. Model version equivalents are in the table here.
Product: Xenium In Situ Gene Expression
Last modified: September 10, 2024