Imaging Level 3 (Segments)
Attribute: Image Segmentation Data Type¶
| Valid Value | Description | Ontology |
|---|---|---|
| Mask | A segmentation output represented as a binary or labeled raster image in which pixels belonging to a segmented object (e.g., a cell or nucleus) are assigned a non-zero/class value and background pixels are assigned zero. | NCIT:C201530 |
| Outline | A segmentation output represented as the boundary contour line surrounding a segmented object, as opposed to a filled area (mask) or a single coordinate (point). | NCIT:C70749 |
| Polygon | A segmentation output in which an object's spatial extent is represented as a closed polygon defined by an ordered sequence of vertex coordinates. | NCIT:C85402 |
| Probability Map | A segmentation output in which each pixel is assigned a continuous value representing the estimated probability that it belongs to a given object class, typically produced by a probabilistic or machine-learning-based segmentation algorithm rather than a binary mask. | Not available |
| Point | A segmentation output in which an object or region of interest is represented by a single coordinate (point) rather than an outline, polygon, or mask. | NCIT:C85402 |
Attribute: Image Object Class¶
| Valid Value | Description | Ontology |
|---|---|---|
| Nucleus | A body within the cell, surrounded by a membrane, within which lie the chromosomes, one or more nucleoli, combined with proteins, and exhibits mitosis. | NCIT:C13197 |
| Cytoplasm | The protoplasm of a cell outside the nucleus, bounded by the plasma membrane and containing all of the cell's organelles except the nucleus. | NCIT:C13226 |
| Plasma Membrane | The semipermeable membrane that encloses the cytoplasm of a cell. | NCIT:C13735 |
| Whole Cell | The smallest units of living structure capable of independent existence, composed of a membrane-enclosed mass of protoplasm and containing a nucleus or nucleoid. | NCIT:C12508 |
| Spot | A discrete, localized region of signal (e.g. a fluorescent punctum) identified within an image, distinct from whole-cell or subcellular compartment segmentation. | Not available |
| Other | Different than the one(s) previously specified or mentioned. | NCIT:C17649 |