Split/Merge Resolution TASK-04
Correcting segmentation errors where neurons are incorrectly joined or divided.
Task Overview
What is Split/Merge Resolution?
Split/merge resolution is the targeted correction of specific segmentation errors. A "false merger" occurs when the AI incorrectly joins two separate neurons into one segment. A "false split" occurs when one neuron is incorrectly fragmented into multiple segments. Resolution involves using specialized tools to separate merged neurons or reconnect split fragments.
Why is it Important?
These errors directly corrupt the connectome. A false merger creates phantom connections between neurons that don't actually touch. A false split breaks real pathways and loses connectivity data. Accurate split/merge resolution is essential for the scientific validity of any downstream analysis.
Key Objectives
- Identify the exact location of segmentation errors
- Determine whether the error is a split or merge
- Apply the correct operation with minimal collateral changes
- Verify the fix resolves the error without creating new ones
- Track ID changes through the edit history
Current Standard Operating Procedure Authoritative
Split Operation Workflow
Use when two neurons are incorrectly merged together:
- Navigate to the merge location (where the two neurons touch)
- Identify the boundary between the two neurons in the EM
- Select the split tool in WebKnossos/FlyWire
- Place split points on either side of the boundary
- Execute the split operation
- Verify the two resulting segments are now separate
- Check that no additional unintended splits occurred
Merge Operation Workflow
Use when one neuron is incorrectly split into fragments:
- Identify the two (or more) fragments that belong together
- Navigate to the gap location
- Verify in the EM that continuity exists (same neuron)
- Select the merge tool
- Click on each fragment to select them
- Execute the merge operation
- Verify the resulting segment is continuous
ID Tracking
Every split/merge operation changes root IDs in the CAVE database. After any edit:
- Record the old ID(s) and new ID(s)
- Update any spreadsheets or tracking documents
- Use the ID validation tool to verify changes propagated correctly
Quality Criteria
- No residual connections between split neurons
- No gaps in merged neuron reconstructions
- ID changes properly tracked and documented
- No unintended edits to neighboring structures
Historical SOPs Archived
Previous split/merge protocols are preserved here for reference. Always use the Current SOP above.
Version History
-
v1.0 (Current) — 2025
Standard split/merge workflow for FlyWire and BANC
Visual Examples
Reference images showing merge and split errors before and after correction.
Error Identification Reference
- False Merger Signs — Sudden color change, anatomically impossible connection, process going "wrong direction"
- False Split Signs — Abrupt ending, nearby orphan fragment, process clearly continues in EM
Common Failure Modes
- Splitting at wrong location Carefully identify the actual merge point in EM before splitting. Splitting too far from the error creates orphan fragments.
- Merging non-continuous segments Always verify EM continuity before merging. Two nearby fragments aren't necessarily from the same neuron.
- Creating new errors with fix A split can accidentally separate parts of the same neuron. Always verify the result after each operation.
- Forgetting to track ID changes Every edit changes IDs. Document changes immediately or they'll be lost in the edit history.
- Operating on stale data Refresh the view before editing. Another user may have already fixed the error or made conflicting changes.
Tools Used
WebKnossos
Primary split/merge interface with EM overlay
FlyWire
Collaborative editing with real-time sync
CAVE
Backend tracking all edits and ID changes
Neuroglancer
3D visualization for verification
Key Commands
- Split tool — Select supervoxels to separate
- Merge tool — Select segments to join
- Undo — Revert last operation (time-limited)
- History — View edit log for a segment
Training Videos
Related Publications
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FlyWire: Online community for whole-brain connectomics