In the link above, I’ve marked the two parts of the axon that are sheathed, with boxes around the ‘starting’ zones.
What I find fascinating here is that there is a segment in the middle here that is NOT protected. It stretches between two relatively “close” branches off the axon. Does this have something to do with these sending signals in different directions along the branch?
Axons send signal in only one direction, away from the soma. The demyelination is interesting! Typically they myelinate to speed up the transmission of an action potential so that it can cover a long distance. But they generally have to demyelinate before they can form synapses with their downstream target cells.
Here’s a fun fact: Myelin is so good at speeding up nerve signals that it can increase their transmission speed from about 1 meter per second in unmyelinated fibers to over 120 meters per second in myelinated ones—that’s faster than the top speed of a cheetah!
As far as I’m aware it usually means the end of the dataset. You can glance at the coords of the z plane if you are near something like this, the dataset ends at 2140, that should should give you a clue
I believe, @annkri is talking about all the white patches, that should be grayed out, as they don’t belong to the trace being cut. At least, in Flywire and BANC they were grayed out. Here, it seems, only other segmented traces are being darkened, while parts without any segmentation remain light.
It has to do with “Segment 0” which is part of a mask to hide connective membrane tissue between the defined segments. It shouldn’t be showing up even when you’re in Multicut mode… I’m reporting this to the dev, Chris to hopefully figure out a fix!
If you would like to not see it during Multicut, you can try “unhiding” Segment 0 during Multicut (see attached screenshot to find the checkbox to click off). However, that makes Segment 0 selectable and visible in regular mode which I find to be more frustrating.
yeah if not mistaken and they’re what i think they are they are segments with ID 0 (if you go to render you’ll see an option ticked that hides segs with ID 0, if you unclick it then you can select those but you cant merge or split them, and from my experience in BANC they show as pure white in 2D when you try to split stuff which can be confusing.
Might have been answered already but I start on a segment that has a merger, I know I am to trace both (let us assume that it’s 2 neurons merged or however many) split neurons, but if on the process of tracing 1 or both of them I come upon more merged stuff, am I supposed to also trace all of those or can I discard those once split?
Good question! Yes, the latter statement – in the process of tracing the “original segments” if you come upon more merged stuff you can discard those “secondary” segments once split.
Eep! Good catch “Find Path” is definitely missing in the play.pyr.ai link. I talked to Chris (dev) and it seems that the landing link may have an old ng state saved and is causing some of the issues we’re encountering… I’ll let him know about this.
For the moment, you can copy your segment IDs and paste them into this link here which has the Find Path working for CA3. It doesn’t have the profile unfortunately, but this will do if you have a complex merger and need this tool.
Question: I have picked a ‘segment’ that is a mergerfest and some of the newly split segments from the origin segment are ‘gibberish’, either glia or stuff that can’t be attached to other neurons (too badly damaged EM and/or super white etc), do I press the star on them and remove them or keep them in the final link I’ll paste in the gsheet but w/o proofreading them?
You can feel safe to remove these from your list of segments once you have cut whatever is useful to you away from them, I usually make it a point to hide them as soon as they load and then un-star anything hidden from my list once I reach the edge.
! Sorry!