What are these granules?

Questions
#1

Often I’ll see granules embedded in dendrites, like this:



They appear and disappear. Are they organelles? Mitochondria? I’ve noticed that the AI almost always fails to route around the granules, and if the AI were updated, this would probably be a major source of improvement.

#2
Things can look different if adjacent slices are taken into account, but as far as we can tell from this single image, these seem 'dotty-er' (as you referred to them as granules) compared to the smear over a certain region which I thought of as mitochondria in 
http://forum.eyewire.org/discussion/65/what-are-these-shell-things#Item_2
so I'd rather assume that these are the vesicles.

The development of next version of AI is on its way close to the end. Hopefully we can apply it in a few weeks.