08 Segmentation and Proofreading

Technical Training: Nanoscale Connectomics

Session outcomes (60 minutes)

• Classify merge, split, boundary, and identity errors reproducibly.
• Prioritize corrections by expected scientific impact.
• Connect proofreading actions to quantitative QC metrics.

Pedagogical arc

• Model: error taxonomy + live correction logic.
• Practice: triage and correction on mixed cases.
• Consensus: adjudicate borderline errors.
• Check: correction log with metric rationale.

Why proofreading is scientific QC

• Correction policy determines analysis validity.

Error taxonomy visual

• Enforce explicit error-class coding in logs.

Ultrastructure-informed correction

Synapse-aware correction checks

Organelle-assisted disambiguation

Boundary failure case

• Show when to stop and escalate instead of over-correcting.

Identity-sensitive correction context

Metrics and release gates

• VI
• edge precision/recall
• ERL
• synapse-centric F1

Operational proofreading loop

1. Triage by expected downstream impact.
2. Correct with local + global consistency checks.
3. Update targeted metrics.
4. Route unresolved cases for adjudication.
5. Gate release on predefined thresholds.

Misconceptions to correct

• “Fix easiest errors first.”
• “Global metric improvements guarantee biological validity.”
• “Automation removes need for human policy.”

Activity

Submit one correction log containing:

• error class,
• before/after rationale,
• metric impact expectation,
• confidence and escalation status.

Rubric checkpoint

• Pass: correction decision tied to error class and metric logic.
• Strong: priority ranking aligned to scientific impact.
• Flag: edits without audit trail or rationale.

External paper figure integration

• Januszewski et al. 2018 FFN architecture/performance figures.
• Segmentation benchmark (CREMI-style) error/metric figures.
• Human-machine proofreading workflow figures from open platforms.

External inserted figure pair (open license)

• Source URLs:
  • https://commons.wikimedia.org/wiki/Special:FilePath/Image-segmentation-example.jpg
  • https://commons.wikimedia.org/wiki/Special:FilePath/Image-segmentation-example-segmented.png
• License: CC0 1.0 Universal Public Domain Dedication.

References and attribution

• Internal visuals: Pat Rivlin + outreach module14 assets.
• Journal-club tie-in: https://doi.org/10.1038/s41592-018-0049-4