How do I crop out a region of interest from the spatial embedding of my Seeker data?

• We recommend using free software called ExCellxGene. You can use a lasso tool to identify cell barcodes in a region of interest. See our official tutorial here: https://knowledgebase.curiobioscience.com/bioinformatics/excellxgene/ 

• Alternatively, Seurat has an interactive plotting function: 

https://satijalab.org/seurat/articles/visualization_vignette#interactive-plotting-features 

Note: FeaturePlot, DimPlot should be used instead of SpatialFeaturePlot SpatialDimPlot, as shown below: 

FeaturePlot(sobj, reduction=“SPATIAL”, features=c(“Actb”)) 

DimPlot(sobj, reduction=“SPATIAL”)