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.
Features
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.