Standard Operating Procedures

Official procedures for Ground Truth annotation, verification, and quality control. Each SOP is the current, authoritative version and carries its own version history and change log.

Standard Operating Procedures (SOPs) define how we carry out the core, repeatable parts of our annotation work, so that results stay consistent and traceable across tracers, datasets, and tools. Pick a procedure from the list on the left, or follow a link below.

Current procedures

What we use now, in WebKnossos.

  • GT Task HandlingSOP-001
    Workflow for handling Ground Truth (GT) tasks from assignment through submission and review.
  • Voxel Painting Cell SegmentationSOP-006
    Our current Ground Truth method — producing voxel-painted training data for the cell-segmentation pipeline.

Recent procedures

Recent guidance that is still largely current.

Older procedures

Procedures for tools we don't routinely use now (e.g. VAST, Omni). Still valid — kept on hand in case we return to them.

  • GT VerificationSOP-002
    How completed Ground Truth tasks are verified before acceptance (VAST / Omni).
  • GT ChecklistSOP-003
    The segmentation checklist to confirm before marking a task complete.
  • File NamingSOP-004
    Naming conventions for annotation files, exports, and datasets.

Versioning

Every SOP keeps its history. Links always point to the current version; deprecated versions remain available from each SOP's version history and are never deleted. Fully retired tooling (for example the standalone Omni and VAST programs) lives in the Archive.