Skeletonization
What is Skeletonization?
Skeletonization creates skeletal (centerline) representations of neuron morphology from 3D segmentations. These skeletons capture the branching structure and spatial extent of neurons in a compact format useful for analysis.
This is not a frequent manual task — skeletonization is usually automated using algorithms like TEASAR or Kimimaro. When manual work is needed, it typically involves reviewing and correcting automated skeletons rather than tracing from scratch.
When Manual Correction is Needed
- Automated skeleton missed thin processes or terminal branches
- Incorrect branch point topology (wrong connections)
- Centerline drifted outside the segmentation in curved regions
- Skeleton extends beyond the actual segmentation boundary
- Node density is too sparse to capture morphological features
Tools Used
Output formats: SWC, JSON, Precomputed meshes
Purpose
Explain skeletonization — creating skeletal (centerline) representations of neuron morphology from 3D segmentations.
Scope
Skeletonization is usually automated (TEASAR / Kimimaro); manual work is mostly reviewing and correcting automated skeletons rather than tracing from scratch. This guide covers when and how that manual correction happens.
Original documentation
The source material this guide distills — original team docs kept here for reference.