get masks related to segments?

[eyaler]

given a segmented skeleton and a mask on which the skeleton was applied, is there a way to get back separate masks of the pixels associated with each of the found segments? btw, plantcv is amazing!

[eyaler]

i found fill_segments() which seems to do what i want be, it uses a builtin thickness=5, which would give me larger masks

[nfahlgren]

Thanks @eyaler!

In fill_segments the segment contours are drawn as a binary mask with a thickness of 5 to use as markers (seeds) for watershed segmentation. The resulting segment masks are derived from watershed and not directly from the initial segment contours - so in theory the drawing thickness should not increase the size of the masks. But maybe it would if your segments are thin to start with?

If it would help, we could make the line thickness controllable through pcv.params.line_thickness as we do with other visualization functions.