plantseg boundaries

[tischi]

Hi,

We are having quite nice plantseg boundaries, but it seems that ultrack sometimes produces a "funny" segmentation:

Do you have a suspicion why the cell in the center could only be segmented half?

[JoOkuma]

This is a hierarchical watershed artifact. Regions' "flat" intensities create arbitrary partitions that are, most of the time, a straight line.

You have three options to fix this:

• increase min_area parameter, so these regions get removed. However, if you have objects with varying areas, this might be challenging and lead to undersegmentation.
• increase min_frontier; this is my preferred option when you have a high accuracy network as plants. This merges regions whose average intensity between them is below min_frontier. In this case, assuming your boundary is between 0 and 1, min_frontier=0.1 or even 0.05 should work. I'm a bit careful to not increase this too much because it could merge regions where cells are shared by a "weak" boundary.
• another option is to blur the boundary map so you avoid creating regions with "flat" intensities. This follows the same reasoning for using EDT to run watersheds. This works better for convex objects. And remember to renormalize the intensity values if using this with min_frontier.

[tischi]

Awesome! min_frontier sounds super useful!

[JoOkuma]

I'll leave this open until we add into the FAQ