Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows
Stockholm University · Science for Life Laboratory · +6 more institutions
Abstract
The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10x Genomics, capable of mapping hundreds of genes in situ at 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 25 Xenium datasets generated from multiple tissues and species, comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open-source computational tools, when applied to Xenium datasets, in…
Citation impact
- FWCI
- 50.18
- Percentile
- 100%
- References
- 66
Authors
19- SMSergio Marco SalasCorresponding
Stockholm University, Science for Life Laboratory, Helmholtz Zentrum München
- LBLouis B. Kuemmerle
Helmholtz Zentrum München
- CMChristoffer Mattsson-Langseth
Stockholm University, Science for Life Laboratory
- STSebastian Tismeyer
Berlin Institute of Health at Charité - Universitätsmedizin Berlin
- CAChristophe Avenel
Uppsala University, Science for Life Laboratory
Topics & keywords
- Computer science
- Workflow
- Preprocessor
- Benchmark (surveying)
- Scalability
- Identification (biology)
- Data mining
- Domain (mathematical analysis)