Interactive selection of cells in spatial data for covariate assignment?

[alexwskh]

Hello,

I have a spatial dataset that I have successfully run RCTD on. I was hoping to get some advice on selecting pixels within areas to define as the explanatory variable.

I am interested in subdividing the mustard blob (a tumour in our animal model) based on a few things. For example I'd like to see if the interior of the blob has different gene expression compared to the periphery. Also if certain regions of interest exhibit different gene expression (presumed vasculature areas).

I'm not really sure how to subset those areas. Is there any interactive packages that would allow me to simply draw on the plot and extract the pixel names to assign to the explanatory variable vector?

Alternatively, is this something I could tease out with cell-to-cell application of CSIDE? Are you able to use unassigned cells as a covariate this way?

Thank you for any help.