The paper is now published:
Long, M., Hu, T., Wang, W., et al. Comparing Xenium 5K and Visium HD data from identical tissue slides from a pathological perspective. Journal of Experimental & Clinical Cancer Research 44, 219 (2025). https://doi.org/10.1186/s13046-025-03479-4
Full text: https://jeccr.biomedcentral.com/articles/10.1186/s13046-025-03479-4
Details of the datasets used in this study are provided in the Online Methods section of the paper.
For convenience, they are summarized below.
All datasets were obtained from the 10x Genomics website:
-
Lung cancer (Visium HD):
Visium_HD_Human_Lung_Cancer_post_Xenium_Prime_5K_Experiment2
https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt -
Lung cancer (Xenium):
Xenium_Prime_Human_Lung_Cancer_FFPE_outs
https://www.10xgenomics.com/datasets/xenium-human-lung-cancer-post-xenium-technote -
Colon cancer:
- Visium HD dataset (Visium HD, Sample P2 CRC)
- Xenium In Situ dataset (Xenium In Situ, Sample P2 CRC)
https://www.10xgenomics.com/platforms/visium/product-family/dataset-human-crc
All custom analysis scripts developed for this study are available in the public repository:
👉 https://github.com/hutaobo/Xenium_5K_Visium_HD_Compare
Processed Visium HD datasets (segmented outputs generated with Space Ranger) have been archived on Zenodo:
👉 https://zenodo.org/uploads/15722536
For any questions regarding the code or data, please contact Mengping Long at [email protected].