Annotations
Biom provides a full annotation system for marking up your data with shapes, text, segmentation masks, and comments.Annotation types
| Type | Description |
|---|---|
| Point | Single point marker |
| Line | Line segment between two points |
| Rectangle | Rectangular region |
| Circle | Circular region |
| Polygon | Multi-point closed polygon |
| Freehand | Freehand drawn shapes |
| Text | Text labels at specific positions |
| Mask | Segmentation masks from model outputs |
Annotation scoping
Annotations can be scoped to:- Per Z-slice — visible only on a specific Z-plane
- Per time-point — visible only at a specific time
- All slices — visible across the entire Z-stack
Annotation features
Styling
- Fill color, stroke color, stroke width, and opacity
- Per-annotation style customization
Organization
- Z-order management — bring to front, send to back, move up/down
- Per-pane visibility — the same annotation can be shown or hidden independently per pane
- Copy across documents — copy annotations between different files
Segmentation metadata
Annotations from model outputs (like SAM3) include:- Instance ID
- Class label
- Confidence score
- Model name that generated the annotation
Document model
Annotations are organized into documents (collections):- Documents can be scoped to a tab or pane
- Multiple documents per pane, switchable
- Persisted locally in IndexedDB
Comments
Biom supports threaded comments attached to specific locations in your images:- Position-linked — comments are tied to a specific view state and location
- Threaded replies — reply to comments to create discussions
- Resolve/unresolve — mark comments as resolved when addressed
- Per-pane modals — comment panels are independent per pane
- Server persistence — comments sync to the server for shared workspaces
- Read-only in shares — viewers can read but not add comments on shared links
Keypoint labeling
Biom includes a dedicated keypoint annotation workflow designed for creating DeepLabCut training datasets:- Session-based — create labeling sessions with defined keypoint schemas
- Frame navigation — step through video frames or image stacks
- Individual keypoint selection — click to place each keypoint
- Undo/redo — full history stack for corrections
- Color palettes — customizable keypoint colors
- Export — export labeled keypoints for model training