CellSegmentation

One Xenium bundle encopasses one sample

• run runBaysor.xenium.sh

One xenium bundle includes multiple samples

• convert parquet to .csv first
• run the split.FOV2Sample.transcriptCSV.py to split the transcript.csv for every sample (given FOV2sample file)
• for every sample, run runBaysor.xenium.sh
• combine the json and segmentation.csv

Sopa-Baysor Cell Segmentation Pipeline

Perform cell segmentation with Sopa and Baysor on Xenium bundles and output updated Xenium bundles with new cell segmentations. Baysor is a cell segmentation tool based on transcriptional composition. Sopa is a tool that enables effieient processing and analyses of spatial omics data. We develope this pipeline to improve cell segmentations from Xenium in an more efficient way. It is faster and uses less memory than directly using Baysor. Details are in subfolders.

References

Baysor

• Petukhov V, Xu RJ, Soldatov RA, Cadinu P, Khodosevich K, Moffitt JR & Kharchenko PV. Cell segmentation in imaging-based spatial transcriptomics. Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-01044-w

Sopa

• Blampey, Q., Mulder, K., Gardet, M. et al. Sopa: a technology-invariant pipeline for analyses of image-based spatial omics. Nat Commun 15, 4981 (2024). https://doi.org/10.1038/s41467-024-48981-z