Proofreading TASK-02
Verifying and correcting AI-generated neuron segmentations for accuracy.
Task Overview
What is Proofreading?
Proofreading is the process of manually reviewing and correcting automated neuron segmentations. AI models generate initial segmentations that often contain errors— neurons incorrectly merged together or split into fragments. Proofreaders identify and fix these errors to produce accurate reconstructions.
Why is it Important?
Proofreading is the critical quality control step that transforms raw AI output into publication-quality data. Even small errors can propagate through downstream analysis, affecting connectivity maps and scientific conclusions. Accurate proofreading ensures the integrity of the entire connectome reconstruction.
Key Objectives
- Identify false mergers (two neurons incorrectly joined)
- Identify false splits (one neuron incorrectly fragmented)
- Apply corrections using split and merge operations
- Verify reconstruction completeness at branch points
- Flag uncertain regions for expert review
Current Standard Operating Procedure Authoritative
Three-Round Triage System
Proofreading follows a structured three-round approach to systematically improve neuron reconstructions while efficiently allocating reviewer time.
Round 1: Quick Scan
- Load the assigned neuron in Neuroglancer/WebKnossos
- Quickly scroll through the entire reconstruction (30-60 seconds)
- Identify obvious large errors (major mergers, missing branches)
- Note any suspicious regions for detailed review
- If neuron appears catastrophically wrong, flag for expert review
Round 2: Systematic Review
- Start at the soma (cell body) if visible
- Follow each major branch outward to terminals
- At each branch point, verify all children belong to the same neuron
- Look for discontinuities suggesting false splits
- Check for color changes suggesting false mergers
- Apply split/merge corrections as needed
Round 3: Verification
- Review all corrections made in Round 2
- Verify the neuron has anatomically plausible morphology
- Check terminal endings reach appropriate targets
- Submit for QA review when satisfied
Quality Criteria
- No visible false mergers with adjacent neurons
- All major branches connected (no orphan fragments)
- Morphology consistent with expected neuron type
- Uncertain regions properly flagged
Source Document
Historical SOPs Archived
Previous proofreading protocols are preserved here for reference. Always use the Current SOP above.
Version History
-
v2.0 (Current) — January 2026
Three-round triage system, updated for WebKnossos -
v1.0 — 2025
Original single-pass proofreading protocol
Archived Documents
Visual Examples
Reference images showing common error patterns and correct reconstructions.
Error Pattern Quick Reference
- False Merger — Two differently-colored processes touch but shouldn't connect
- False Split — A process abruptly ends where it should continue
- Missing Branch — Branch point exists but one child is missing
- Extra Fragment — Isolated piece that should be merged or deleted
Common Failure Modes
- Missing small branches Fine processes are easy to miss. Always check branch points carefully and follow each child to its terminal.
- Accepting AI-generated mergers Don't assume the segmentation is correct. Verify that connected segments actually belong to the same neuron.
- Over-splitting at ambiguous regions When unclear, flag for review rather than splitting. False splits are harder to fix later than false mergers.
- Ignoring crossing fibers Where processes cross (but don't synapse), verify they're correctly separated. This is a common merger location.
- Rushing Round 1 The quick scan should still be thorough enough to catch major errors. Don't skip regions entirely.
Tools Used
WebKnossos
Primary proofreading platform with split/merge tools
Neuroglancer
3D visualization for verifying reconstructions
CAVE
Backend database storing segmentation edits
FlyWire
Collaborative proofreading interface
Key Operations
- Split — Separate incorrectly merged segments
- Merge — Join segments belonging to same neuron
- Undo — Revert recent edit if mistake made
- Flag — Mark uncertain region for expert review
Training Videos
Additional Videos
- Synapse Identification (for context) (Local file)
Related Publications
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FlyWire: Online community for whole-brain connectomics