Glossary
Plain-language definitions of the jargon used across the tracer docs — anatomy, imaging artifacts, and annotation terms. Where a term has a current protocol, it links straight to it.
Annotation
Marking or labeling structures in image data — painting voxels, tracing, tagging, or otherwise recording what is where. The umbrella term for most of the team's ground-truth work.
Bounding box
The 3D box defining the extent of your assigned volume — the borders within which you segment. Often called the volume border; watch its edges for small segments that just barely pass through.
Defects
Imaging artifacts and tissue-quality problems — cracks, folds, tears, fat globules, membrane swirls, missing slices, and staining issues. They should not be mistaken for biological structure.
Current protocol → WebKnossos - GT Semantic Segmentation Protocol (SOP-006) — defect segmentation & masking.
ER (Endoplasmic Reticulum)
A membrane network inside cells — an internal organelle. It can be mistaken for a separate object or boundary, so investigate carefully before segmenting around it.
Extracellular space
The space outside cells. Under the older Omni-era checklist this was collapsed into a single segment; defer to the current protocol for how it is handled today.
Fat globule
A lipid-droplet artifact in the EM tissue. Color it separately and as accurately as possible rather than absorbing it into a neighboring cell.
Current protocol → WebKnossos - GT Semantic Segmentation Protocol (SOP-006) — defect labels.
Invaginations
Infoldings of a cell membrane that push inward into the cell. They are easy to misread as a separate object or as a boundary between cells — look closely before splitting.
Membrane swirl
A swirled or whorled membrane artifact (also described as ER-membrane swirling). Segment it separately rather than letting it merge into surrounding structure.
Current protocol → WebKnossos - GT Semantic Segmentation Protocol (SOP-006) — defect labels.
Myelin
The insulating sheath that wraps axons, formed by glial cells. In current semantic segmentation we distinguish the inner tongue (the innermost wrap, next to the axon) from the outer tongue (the outermost wrap, on the glial side). Plain "myelin" is still a valid label when the inner/outer distinction is ambiguous.
Current protocol → WebKnossos - GT Semantic Segmentation Protocol (SOP-006) — myelin segmentation.
Organelles
Internal cell structures such as mitochondria and ER. Be careful not to mistake an organelle for a separate cell or for a boundary when segmenting.