Why this unit

Process-type misclassification is a major source of downstream graph error.

Learning goals

• Distinguish axons and dendrites with morphology + organelle cues.
• Handle ambiguous edge cases with confidence scoring and continuity checks.

Core technical anchors

• Combined cue strategy: morphology, organelles, local connectivity.
• Edge cases: en passant boutons, thin dendrites, truncations.
• Auditability via confidence and correction logs.

Method deep dive: axon-vs-dendrite classification

1. Morphology pass: Branch caliber, tortuosity, spine presence, and process tapering.
2. Organelle pass: Vesicle clustering, microtubule patterning, mitochondrial distribution.
3. Connectivity pass: Input/output pattern and bouton/spine relationships in neighborhood.
4. Continuity pass: Validate interpretation along additional slices and branch points.
5. Decision logging: Capture confidence and alternative hypothesis if ambiguous.

Quantitative QA checkpoints

• Confusion matrix for axon/dendrite labels against adjudicated truth set.
• Error concentration map by tissue region and annotator.
• Rework fraction: percent of labels reversed during secondary review.
• Downstream sensitivity: impact of class errors on motif counts and graph metrics.

Frequent failure modes

• Thin dendrites mislabeled as axons: Add local synaptic-role evidence before finalizing.
• Truncated field-of-view bias: Mark as provisional when continuity evidence is missing.
• Bouton-centric bias: Avoid relying only on vesicle presence without full context.
• Inconsistent team criteria: Calibrate weekly with shared edge-case panels.

Visual training set (draft)

Attribution: Pat Rivlin training materials (MICrONS proofreading deck). Some manifest-listed IDs used in planning (`S04`, `S06`, `S10`, `S16`) were not present in extracted thumbnails and were replaced with available neighboring cues.

Course links

• Existing overlap: module04, module09
• Next unit: 07 Glia

Practical workflow

1. Start with morphology cues.
2. Add organelle and synaptic-context checks.
3. Verify continuity in neighboring sections.
4. Assign class with confidence and review note.

Discussion prompts

• Which edge cases most frequently produce classifier disagreement?
• How should teams calibrate confidence thresholds for class assignments?

Related resources

• Journal club list: Technical Track Journal Club
• Shared vocabulary: Connectomics Dictionary

Quick activity

Choose one ambiguous process and document the three strongest cues you used to classify it.

Draft lecture deck

• Slide draft page: Axons and Dendrites deck draft