Standard Operating Procedures

Standard operating procedures and task guides for the team's annotation work — segmentation, proofreading, labeling, verification, and file conventions. Includes current WebKnossos protocols and older VAST / Omni-era methods kept for reference.

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.

  • WebKnossos - GT Segmentation Task HandlingSOP-001
    The where & which — how to pick up, run, and hand off a Ground Truth task. The what & how for the current task lives in Voxel Painting (SOP-006). A task is assigned as a Volume in three parts, done in turn: cell segmentation, mitochondria, and defects (e.g. vol4-cell-seg, vol4-mito, vol4-defects).
  • WebKnossos - GT Semantic Segmentation ProtocolSOP-006
    Our current WebKnossos Ground Truth task — the three-part volume (cell segmentation, mitochondria, defects). Holds the per-part rules: what and where to paint, the semantic classes for each part, edge cases, and how to handle uncertain labels.

Recent procedures

Recent guidance that is still largely current.

  • WebKnossos - General GT Protocol GuidelinesSOP-005
    Guidelines for the Voxel Painting Cell Segmentation task. Filed under Recent because minor changes may have landed since, but it's still roughly 90–95% accurate.

Older procedures

Written around earlier tools (VAST, Omni), but the principles and conventions still apply today.

  • General GT Verification/ReviewSOP-002
    The general review guide — how to tell when your own or someone else's work is actually done and correct. Tool-agnostic principles; the examples use the older VAST / Omni workflows.
  • Old Omni ChecklistSOP-003
    A general how-to checklist to run through before marking a task complete.
  • File NamingSOP-004
    Naming conventions for annotation files, exports, and datasets. Written in the Omni era but largely translatable today — with newer conventions to be added.

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.