Axon structure in zfish dataset
Blah blah blah
Red = axon (long horizontal line = "main branch", vertical lines = "side branches")
Green = soma (cell body) and dendrites
Blue arrow = starting branch of axon
Orange arrows = where the starting branch splits into 2 directions and becomes the main branch (the whole horizontal red line) of the axon
Black arrows = side-branches of axon
This diagram is pretty simplified and is meant to show typical axon structure, saying nothing about the dendrites or soma. The main ideas about zfish axon structure are:
1) An axon starts as a branch (see blue arrow in diagram above) coming off of the stem or not far from where the stem splits into trunks, and at some point, this branch will split and continue in 2 opposite directions (like the bottom of a T becoming the top of the T) (orange arrows in diagram), each traveling a long distance. I usually call this long branch (the top of the T, extended in both directions) the "main branch" of the axon. (This is the long, squiggly horizontal line in the diagram.)
2) An axon (that is, the main branch) will usually have "side-branches" (indicated by the little black arrows) that come off of it at (very roughly) evenly spaced intervals. The side branches may vary in length (sometimes they are so short that they are more like "side-nubs"!), sometimes within the same cell, and they may or may not have further branches of their own. Sometimes we won't encounter any side branches visible within the dataset.
3) An axon does not seem to care about the dendrite tree; it may cut right through it and even send off side-branches through it and make things look messy. Or it may travel somewhere away from the dendrite tree. The axon just simply goes where it pleases, whether the dendrite tree is in its path or not.
Over time, I will try to add example screenshots of real axons to illustrate the points listed above.
Zfish cells almost always start out as axons, and because axons are long, many times the rest of the cell is outside of the dataset, so in these common cases all you will see is an axon.