The terminology spot swapping[1] describes the artifact for spatial data that mRNA bleed from nearby spots causes substantial contamination of UMI counts. Spot clean in Flow is a task that aims to improve estimates of expression by correcting for spot swapping.

The task can only be invoked from the Space ranger task output data node since It takes the raw count matrix as input. To run the Spot clean task in Flow:

• Click the Single cell counts outputted from Space ranger (Figure 1)
• Click Pre-analysis tools in the toolbox
• Click Spot clean
• Click Finish to run the task with default settings
  

Another single cell counts node will be generated. The data node contains a matrix of cell counts with the decontaminated gene expressions (Figure 2).

The Cell counts data node is a counts type data node and downstream analysis tasks, such as normalization, PCA, and ANOVA, can be used to analyze the group cell counts data. 

References

1. Ni, Z., Prasad, A., Chen, S. et al. SpotClean adjusts for spot swapping in spatial transcriptomics data. Nat Commun 13, 2971 (2022). https://doi.org/10.1038/s41467-022-30587-y