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Proofreading Tool

The proofreading tool lets you fix merge and split errors in segmentations generated by automated workflows (outside WEBKNOSSOS), for example with Voxelytics. Split and merge operations are executed directly on the underlying supervoxel graph structure.

Watch this video to get started with the proofreading tools:

To use the proofreading tool, enable an ID mapping for your segmentation so WEBKNOSSOS can load the supervoxel graph. Once detected, you can activate the proofreading tool from the toolbar (clipboard icon):

  1. Select an ID mapping for a segmentation layer from the left-hand side panel
  2. From the toolbar, switch to the proofreading tool (clipboard icon)
  3. [Optional] Press Shift + middle-click on any segment to load and display its supervoxel graph
  4. Proceed to fix split and merge errors:

Fixing Split Errors

  1. Left-click on any part of the source segment. It will be marked with a white crosshair
  2. Right-click on the target segment to bring up the context menu. Select Merge With Active Segment
  3. WEBKNOSSOS will merge both segments and reload the updated segmentation and 3D meshes

Fixing Merge Errors

  1. Left-click on any part of the source segment. It will be marked with a white crosshair
  2. Right-click on the part of the source segment that you would like to split off to bring up the context menu. Select Split from active segment (Min-Cut)
  3. WEBKNOSSOS will perform a min-cut operation to delete all supervoxel graph edges between the source and target segments, effectively splitting the two into individual segments
  4. WEBKNOSSOS will split both segments and reload the updated segmentation and 3D meshes

Proofreading operations rely on the quality of the initial over-segmentation. If cells are already connected incorrectly in that base graph, WEBKNOSSOS cannot separate them with proofreading alone.

If you want to reload, hide, or remove a 3D mesh during proofreading, use the mesh context menu in the 3D viewport.

Proofreading Toolbar Controls

When the proofreading tool is active (and editable mappings are enabled), additional controls are available in the toolbar:

  • Clear proofreading by-products: Removes auxiliary meshes loaded during proofreading.
  • Automatic mesh loading: Toggles automatic loading of meshes during proofreading.
  • Selective segment visibility: Shows only hovered or active segments to reduce visual clutter.
  • Multi split mode: Enables partition-based splitting (can also be toggled with M).

In addition to context-menu actions, you can also modify agglomerate skeletons directly (add/remove nodes and edges) for fine-grained control.

Info

The proofreading tool requires a supervoxel-graph-compatible mapping. These mappings are commonly generated by automated segmentation pipelines (for example, Voxelytics). If you need help preparing compatible files, contact hello@webknossos.org.