Skeletons¶
A skeleton defines the parts you label. It is a set of nodes (body parts) and edges (connections between them), shared by every instance in the project. Everything downstream — training, the quality checks, the rendering — is defined in terms of it.
Starting from a template¶
File ▸ New Project… offers built-in skeletons:
| Template | Nodes |
|---|---|
| Fly | 32 |
| Mouse top-down | 12 |
| Human | 17 |
| C. elegans | 2 |
| Empty — define later | none yet |
Pick the closest one and edit it, or start empty.
Drawing a skeleton on the frame¶
Often the fastest route, because you can see the animal while you do it:
- Open the Skeleton panel and click Draw skeleton on frame.
- 1 · Place nodes — click to place each node where that body part sits. Drag a placed node to move it, and double-click it to rename it.
- Click Next: Connect edges →.
- 2 · Connect edges — drag a stroke through the nodes you want connected; the stroke becomes edges along the path. Clear edges starts the edges over, and ← Back returns to placing nodes.
- Click Done. The app asks whether to create an instance on this frame from your layout: Create instance or Not now.
Nodes come out named node_0, node_1, … Rename them on the frame while
placing, or later by double-clicking a name in the Skeleton panel.
If the project already has a skeleton, Draw skeleton on frame first asks whether to Edit existing (add to it) or Delete & start new.
Rename before you label
Node names are how you'll read every quality-check finding, every metrics
table, and every exported column. head / torso / tailbase beats
node_0 / node_1 / node_2 immediately and forever.
Editing in the panel¶
The Skeleton panel has three tabs, each with its own buttons:
| Tab | Buttons |
|---|---|
| Nodes | New Node, Delete Node, Delete Skeleton (clear it and start again) |
| Edges | New Edge (pick a source and destination node), Delete Edge |
| Symmetries | New Symmetry (declare a left/right pair), Delete Symmetry |
Symmetries¶
A symmetry marks two nodes as mirror images of each other — left_ear and
right_ear, left_hind_paw and right_hind_paw.
Declaring them is worth the thirty seconds: the Label Quality Check uses symmetries to detect chirality errors, where an instance has left and right systematically swapped. That is one of the most common labeling mistakes and one of the hardest to spot by eye. If you haven't declared symmetries, the check falls back to inferring pairs from node names containing left/right markers.
Loading and saving skeletons¶
Load From File… in the Skeleton panel reads a skeleton out of:
- a
.slpproject - a skeleton JSON file (the legacy SLEAP format)
- a skeleton YAML file
and Save As writes YAML. This is how you reuse one lab-standard skeleton across many projects.
When you load a skeleton into a project that already has labels, the app compares the two and remaps existing instance points onto the new node set by name, so labels survive a skeleton swap wherever the names still line up.
How many nodes?¶
Fewer than you want. Every node is a point you must place on every instance on every labeled frame, forever. Three to five well-chosen, reliably visible parts get you a working model far faster than a 30-node rig you'll label sloppily.
For top-down models you also need one node that is central and almost always visible, to serve as the anchor part the model crops around. Design the skeleton so such a node exists.