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)


References and attribution