06 Axons and Dendrites

Technical Training: Nanoscale Connectomics

Unit 06 · Axons and dendrites

Session outcomes (60 minutes)

  • Classify neurites using a reproducible multi-cue protocol.
  • Document uncertainty and escalation rationale for edge cases.
  • Quantify classification quality with confusion-style summaries.
Unit 06 · Axons and dendrites

Pedagogical arc

  • Model: expert classifies one neurite live.
  • Practice: pair annotation on mixed-evidence panels.
  • Consensus: adjudication and policy revision.
  • Check: justified final call and uncertainty note.
Unit 06 · Axons and dendrites

Why this unit is high leverage

  • Axon/dendrite identity errors distort connectivity statistics.
  • Misclassification propagates into motif analysis and model priors.
  • Reproducible identity policy is a prerequisite for trustworthy graphs.
Unit 06 · Axons and dendrites

Visual context: morphology baseline

Unit 06 · Axons and dendrites

Visual context: dendritic cue panel

Unit 06 · Axons and dendrites

Classify these profiles, then check

  • Left: raw human cortex. Right: the model's answer key.
  • Blue axon, green dendrite, orange astrocyte — note how many are genuinely hard.
Unit 06 · Axons and dendrites

Real data: excitatory vs inhibitory synapse

  • Matched scale, nothing drawn over either density.
  • At 4 nm a Type I PSD is 8–12 px — the asymmetry is subtle, and the classifier is 85–87% accurate.
Unit 06 · Axons and dendrites

Real data: a myelinated axon

  • Compact myelin reads as a dark annulus at 4 nm.
  • Individual lamellae (12 nm period = 3 px) are NOT resolvable here.
Unit 06 · Axons and dendrites

Visual context: axonal cue panel

Unit 06 · Axons and dendrites

Side-by-side discrimination

  • Ask learners to justify which cue would survive lower image quality.
Unit 06 · Axons and dendrites

Ambiguous process case

  • Train weighted-evidence reasoning, not binary heuristics.
Unit 06 · Axons and dendrites

Continuity check case

  • Require short-path continuity inspection before final call.
Unit 06 · Axons and dendrites

High-complexity edge case

  • Escalate unresolved ambiguity to adjudication queue.
Unit 06 · Axons and dendrites

Operational classification protocol

  1. Initial morphology read.
  2. Synaptic/organellar context check.
  3. Continuity check in adjacent slices.
  4. Confidence assignment.
  5. Escalation if evidence conflict persists.
Unit 06 · Axons and dendrites

Misconceptions to correct

  • "Thin process = axon".
  • "One bouton-like feature determines identity".
  • "Ambiguous means annotator failed".
Unit 06 · Axons and dendrites

Activity

Classify three ambiguous neurites and submit:

  • primary label,
  • cue table,
  • confidence,
  • alternate label and why rejected.
Unit 06 · Axons and dendrites

Rubric checkpoint

  • Pass: label plus two independent cues.
  • Strong: includes continuity evidence and uncertainty logic.
  • Flag: unsupported hard labels.
Unit 06 · Axons and dendrites

External paper figure integration

  • Kasthuri et al. 2015: process morphology examples in dense reconstructions.
  • MICrONS/FlyWire morphology figures for large-scale context.
  • Optional neuroanatomy atlas figure for compartment-level validation.
Unit 06 · Axons and dendrites

External inserted figure (open license)

Unit 06 · Axons and dendrites

References and attribution

Unit 06 · Axons and dendrites