Plotting spatialdata in only one coordinate system

Ecosystem
1

Hi all,

I am trying to work with some CosMX data using the spatialdata package, but I’m having some trouble with plotting. I want to plot 1 FOV with several layers overlaid on top, but I don’t want to plot both the global and local (within FOV) coordinate system.

If I try to select an element using the render_images subroutine, I get an error that the number of elements doesn’t match the number of coordinate systems. How do I specify to only plot images within a specific coordinate system?

Thanks!

2

OK figured it out - if I run transform_to_coordinate_system, the resulting object should render properly in that coordinate system.

3

Hi @conradfoo, sorry for the late answer and glad that you find a solution. Another alternative isn to call sdata.pp.get_elements("local"), which will filter the SpatialData object to the coordinate system you are interested to. You can see an example of this in action in this notebook: Technology focus: MibiTOF — spatialdata