Semantic Segmentation (Labeling)

What is Semantic Segmentation?

Semantic segmentation is the process of labeling tissue types and cellular structures in electron microscopy data. This encompasses two related activities: voxel painting (hand-painting specific structures in 3D) and classification labeling (identifying and naming structures like axons, dendrites, and somata).

We have a storied history of hand-painting neurons, mitochondria, vesicles, synapses, T-bars, errors, membranes, and more. The tools and software have changed rapidly over the years as technology capabilities evolve, but the core skill of identifying and labeling biological structures in EM imagery remains the same.

Structure Labels

Note that the distinction between painting and labeling can be confusing for newer tracers. Painting means coloring in the actual voxels of a structure. Labeling means assigning a classification name (like "axon" or "dendrite") to an already-segmented object.

Defect Annotation

Defect annotation is a specialized form of semantic segmentation focused on marking imaging artifacts, tissue damage, and data quality issues. Defects include section tears, folds, staining artifacts, missing slices, and other preparation problems. Accurate defect annotation prevents these regions from corrupting downstream analysis. See the Gallery for visual examples of common defects.

Procedure

1. Load the assigned volume or task in the annotation tool
2. Orient yourself — identify major landmarks and the region of interest
3. Select the appropriate label/brush for the structure you're painting
4. Paint or label structures systematically, working through Z-slices
5. Cross-check your labels in orthogonal views (XY, XZ, YZ) for consistency
6. Submit for review when complete

Common Failure Modes

• Confusing axons with dendrites in ambiguous cross-sections
• Missing myelin wrapping around processes
• Inconsistent labeling across Z-slices (label drift)
• Guessing in damaged or low-contrast regions instead of flagging
• Boundary leakage when painting — extending labels past structure edges

Tools Used