Welcome to Cell Locator’s documentation!

Cell Locator is a free, open source and multi-platform pinning tool to facilitate mapping samples into common 3D spaces.

A desktop application based on 3D Slicer that displays the Allen Institute for Brain Science CCF or MNI atlas, color segmented by structure of the brain, and allows a user to create a planar polyline annotation to facilitate mapping samples into the corresponding atlas.


  • Create, save, and load spline or polyline based annotation.

  • Manage and save multiple annotations per file.

  • Save annotations as JSON containing Spline or Polyline points as well as orientation and thickness.

  • Download from / Upload to a LIMS system. See LIMS integration

  • 3 interaction modes: Explore, Edit or Place point.

  • Reslicing in arbitrary directions.

  • Ontology selection: layer vs area.

  • Input of Roll/Pitch/Yaw.

  • Load CCF or MNI atlas. See command-line arguments.

Indices and tables