06 Axons and Dendrites

Technical Training: Nanoscale Connectomics

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.

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.

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.

Visual context: morphology baseline

Visual context: dendritic cue panel

Visual context: axonal cue panel

Side-by-side discrimination

  • Ask learners to justify which cue would survive lower image quality.

Ambiguous process case

  • Train weighted-evidence reasoning, not binary heuristics.

Continuity check case

  • Require short-path continuity inspection before final call.

High-complexity edge case

  • Escalate unresolved ambiguity to adjudication queue.

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.

Misconceptions to correct

  • "Thin process = axon".
  • "One bouton-like feature determines identity".
  • "Ambiguous means annotator failed".

Activity

Classify three ambiguous neurites and submit:

  • primary label,
  • cue table,
  • confidence,
  • alternate label and why rejected.

Rubric checkpoint

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

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.

External inserted figure (open license)

References and attribution