What you're seeing in the above code is the number of cells in the first leave clump. To see how many leaf_clumps you have, you would do:

print (len(leaf_clumps))

The message, "Pixelizing contour 391", may be a red herring. Many clumps will get created and destroyed during the clump finding process, but the unique clump id is always increments, so you could end up with 4 clumps with ids of 0, 8, 42, 391, just as an example.

Still, I suspect you'll find that there are an awful lot of leaf clumps, just based on the image you sent. If there is a large number of clumps along the line of sight, then annotate_clumps may always look a bit messy. If you think there are too many clumps, you can try adding a clump_validator to set some lower limits on what should be considered a clump. It may very well be the case that you have a large number of single-cell clumps just due to fluctuations in the density field. Adding some validation criterion, like a minimum number of cells, or gravitational boundedness, may help cut that down.

Britton