Skeleton Builder not finding fully labeled animal

Hi there,

I’ve labeled the first set of videos, and I’m trying to use skeleton builder to connect all my markers. My data is of snakes, so I’m just connecting a single line of markers, but I believe best practice is to connect head to 1 to 2 to etc. and then also head to 2, head to 3, etc, in case 1 or 2 is not visible in a particular frame?

However, when I use skeleton builder from the GUI the image I’m given is only 5 of the markers, even though I have 12 body parts listed in the .yaml file. See screen shot below. I’m getting an error " UserWarning: A fully labeled animal could not be found. m5, m6, m7, m8, m9, m10, vent will need to be manually connected in the config.yaml." but as there are many frames where all 12 markers are labeled, I’m not sure how to interpret this. Thanks!

Hello @grahmich, what version of DLC are you using? I believe this bug was fixed with https://github.com/DeepLabCut/DeepLabCut/commit/045c20479d7ec126a3dc46d4e5fac92a9ced9f48#diff-71f2afe78e5b3f1e100c988b6cfb200f from DLC 2.2b7 on.

I am using 2.2b7; I’ll try updating to 2.2b8

EDIT: still having this problem. I’ve manually entered the skeleton for now, but would be nice to have this feature working for the future.

When you run check labels, can you show us an image with all 12 shown?

The builder works fine for me, I’m worried about the data more so :wink:

Here are some images of all 12 points from 4/5 camera views. I also have one camera view where all 12 points are never visible at the same time – an illustrative frame is also attached (3rd image). Is that the issue? If so, would you suggest not including training data from that view or just manually making the skeleton, as I did for these videos?

Edit: I wanted to mention that I’m also switching back in forth between my personal laptop (to use GUI features) and a lab computer with a GPU, so if there could be an issue caused by going back and forth (like a missing file) that might be it too? Although I did check_labels on the same computer I’m doing skeleton builder on.

That definitely looks like a bug!
I’ll get back to you once I figure why :slight_smile:

All right, I had overlooked the fact that the SkeletonBuilder stops as soon as labeled data are found, which in your case must have been from the view with incomplete annotations. This is fixed with https://github.com/DeepLabCut/DeepLabCut/commit/b1f8f413ec8f5ffdb522624b62a02b5980472f66.