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.
Axon
The output process of a neuron, carrying signals away from the soma toward synapses. In cross-section it is easily confused with a dendrite; a dense cluster of synaptic vesicles is a strong cue that a process is an axon.
Blood vessel
Vasculature running through the tissue. It is segmented separately from neural structures and is a useful spatial landmark, but it is not a neuron.
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.
Classification labeling
Assigning a category name (axon, dendrite, soma, …) to an already-segmented object, rather than painting its voxels. The second core semantic-segmentation activity.
Current protocol → Semantic Segmentation (Labeling)
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.
Dendrite
The input process of a neuron, receiving signals at synapses and often studded with spines. Distinguishing dendrites from axons in ambiguous cross-sections is a common labeling challenge.
Electron microscopy
The imaging modality that produces the high-resolution grayscale volumes tracers annotate; abbreviated EM. Contrast comes from heavy-metal staining of membranes.
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.
Glia
Non-neuronal support cells such as astrocytes, oligodendrocytes, and microglia. Glial cells form the myelin that wraps axons.
Golgi apparatus
A stacked-membrane organelle that packages proteins. Its distinctive parallel cisternae can be mistaken for membrane swirls or defects.
Ground truth
Carefully verified annotations treated as the correct reference, used to train and evaluate automated segmentation. The quality bar for most tracer work; often abbreviated GT.
Current protocol → WebKnossos - GT Segmentation Task Handling (SOP-001)
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
The lipid bilayer bounding a cell or organelle. Membrane boundaries are what you trace when segmenting; painting past a membrane (boundary leakage) is a common error.
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.
Merge error
When the segmentation incorrectly joins two separate objects into one. Fixed by splitting during proofreading.
Mitochondria
Energy-producing organelles found inside axons, dendrites, and somata. Their double membrane and internal cristae make them recognizable; do not mistake a mitochondrion for a separate object or boundary.
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.
Nucleus
The membrane-bound compartment inside the soma that holds the cell's DNA. A reliable marker that you are looking at a cell body rather than a process.
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.
Proofreading
Reviewing and correcting an existing automated segmentation — fixing merge and split errors rather than painting from scratch.
Current protocol → Proofreading 3D (Tracing)
Semantic segmentation
Labeling tissue types and cellular structures in EM data, spanning both voxel painting and classification labeling.
Current protocol → Semantic Segmentation (Labeling)
Skeletonization
Reducing a segmented neuron to a thin centerline (skeleton) that captures its branching structure for downstream analysis.
Current protocol → Skeletonization
Soma
The cell body of a neuron, containing the nucleus; also called the perikaryon. It is the origin point from which axons and dendrites extend.
Split error
When the segmentation incorrectly breaks a single object into multiple pieces. Fixed by merging during proofreading.
Supervoxel
The smallest atomic segment produced by the base segmentation. Neurons are built by agglomerating supervoxels, and ID updates follow supervoxels through splits.
Synapse
The connection point where one neuron signals another. In EM it is identified by a presynaptic vesicle cluster, a synaptic cleft, and a postsynaptic density (or a T-bar in insect datasets).
Synaptic cleft
The narrow gap between the pre- and postsynaptic membranes at a synapse. Its location defines where a synapse is annotated.
T-bar
The T-shaped presynaptic density found at insect (e.g. Drosophila) synapses. It marks the release site and is used to identify and count synapses in fly datasets.
Vesicles
Small membrane-bound transport bodies that cluster at synapses. A dense vesicle pool signals a presynaptic terminal.
Voxel painting
Hand-coloring the individual voxels of a structure in 3D to produce a dense segmentation. One of the two core semantic-segmentation activities, alongside classification labeling.
Current protocol → WebKnossos - GT Semantic Segmentation Protocol (SOP-006)