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.
:maxdepth: 2
:caption: Contents
getting-started.md
app-overview.md
reference-atlases.md
coordinate-systems.md
lims-integration.md
command-line-tools.md
developer-guide/index.md
acknowledgments.md
license.md
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