Hey @DanielAsarnow,
The edges are drawn with line thicknesses proportional to the amount of particles in that connection and normalized wrt the most populous connection (including self connections). Opacity is always 1 (fully opaque), but some lines can appear very faint when their effective thickness is less than 1 pixel. We’re planning on adding some numerical outputs to supplement this visualization, and also adjust for clarity – see this recent discussion with @olibclarke.
Valentin