Skeleton And Network Analysis

Skeleton workflows analyze curvilinear structures such as mitochondria, neurites, vessels, fibers, and similar networks.

Basic QC Workflow

binary mask
  -> Skeletonize
  -> Skeleton Graph Overlay

Use the overlay to check endpoints, junctions, isolated voxels, and branch structure before trusting tables.

Measurement Workflows

Per-component measurements:

binary mask
  -> Skeletonize
  -> Analyze Skeleton

Branch-level measurements:

binary mask
  -> Skeletonize
  -> Measure Skeleton Branches

Branch summaries:

binary mask
  -> Skeletonize
  -> Measure Skeleton Branches
  -> Summarize Skeleton Branches

Whole-network summary:

binary mask
  -> Skeletonize
  -> Measure Overall Skeleton Network

Explicit graph tables:

binary mask
  -> Skeletonize
  -> Skeleton Graph Tables

Cleanup Workflow

binary mask
  -> Skeletonize
  -> Prune Skeleton Branches
  -> Analyze Skeleton / Measure Skeleton Branches

Pruning removes short terminal spurs and optionally isolated skeleton voxels.

Reference Workflows

Workflow	Purpose
synthetic-skeleton-qc.json	Compact 3D skeleton QC with keypoints, branch/component labels, pruning, and tables.
synthetic-advanced-skeleton-network.json	Time-indexed 3D skeleton/network stress test with loops, fragments, graph tables, and anisotropic scale.

What To Check

• Is the input a binary mask or an already skeletonized mask?
• Should analysis be 2D per slice or 3D volumetric?
• Is z-spacing correct before reporting physical lengths?
• Are short spurs biological or threshold/skeletonization artifacts?
• Are endpoint and junction counts plausible in the graph overlay?