Open tischi opened 4 months ago
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:
min_area
parameter, so these regions get removed. However, if you have objects with varying areas, this might be challenging and lead to undersegmentation.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.min_frontier
.Awesome! min_frontier
sounds super useful!
I'll leave this open until we add into the FAQ
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?