APA
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Salas, S. M., Czarnewski, P., Kuemmerle, L. B., Helgadottir, S., Matsson-Langseth, C., Tismeyer, S., … Nilsson, M. (2023). Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows. BioRxiv.
Chicago/Turabian
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Salas, Sergio Marco, Paulo Czarnewski, L. B. Kuemmerle, Saga Helgadottir, Christoffer Matsson-Langseth, Sebastian Tismeyer, Christophe Avenel, et al. “Optimizing Xenium In Situ Data Utility by Quality Assessment and Best Practice Analysis Workflows.” bioRxiv (2023).
MLA
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Salas, Sergio Marco, et al. “Optimizing Xenium In Situ Data Utility by Quality Assessment and Best Practice Analysis Workflows.” BioRxiv, 2023.
BibTeX Click to copy
@article{sergio2023a,
title = {Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows},
year = {2023},
journal = {bioRxiv},
author = {Salas, Sergio Marco and Czarnewski, Paulo and Kuemmerle, L. B. and Helgadottir, Saga and Matsson-Langseth, Christoffer and Tismeyer, Sebastian and Avenel, Christophe and Rehman, Habib and Tiklova, Katarina and Andersson, Axel and Chatzinikolaou, Maria and Theis, F. and Luecken, Malte D. and Wählby, C. and Ishaque, Naveed and Nilsson, M.}
}
The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10X Genomics capable of mapping hundreds of transcripts in situ at a subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore eight preview Xenium datasets of the mouse brain and two of human breast cancer by comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies. In addition, we benchmarked the performance of multiple open source computational tools when applied to Xenium datasets in tasks including cell segmentation, segmentation-free analysis, selection of spatially variable genes and domain identification, among others. This study serves as the first independent analysis of the performance of Xenium, and provides best-practices and recommendations for analysis of such datasets.
