If I have multiple regions or tissues of interest on a tile, how do I select only the beads for the region I am interested in?

One way to do this is through seurat.  It has an interactive plotting function, where you can draw around an area and it will return a list of cells/beads within the boundary you draw. See link below (section interactive plotting features). Please note the vignette describing the two ways to perform interactive plotting.

 

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