TRACER

TRACER enables registration, visualization, and analysis of anatomical data in rodent brains to support planning and interpretation of electrophysiological recordings, viral tracing, and precise anatomical targeting.

Key Features:

• Pre-Experimental Planning: Plan coordinates for implanting electrodes, targeting viral injections, or tracers prior to experiments.
• Electrode and Expression Registration: Register recording electrode locations (e.g., Neuropixels, tetrodes), viral expression patterns, and other anatomical features to atlas space.
• 2D and 3D Visualization: Support visualization of anatomical data in both 2D and 3D formats.
• Atlas-Based Anatomical Delineation: Use annotated 3D volumes from the Waxholm Space Atlas of the Sprague Dawley Rat Brain and the Allen Mouse Brain Atlas for regional delineations.
• Advanced Slice and Transformation Tools: Scroll through digital atlases, create custom-angle slice cuts, and perform free transformations of tissue sections to align with atlas slices.
• 3D Brain Reconstruction: Reconstruct a 3D brain mesh using tissue from individual animals.
• Multi-Injection Analysis and Cell Counting: Delineate expression patterns from multiple injections across sections and provide individual cell counts.

Scientific Applications:

• Electrophysiological recording planning and analysis: Map and interpret electrode recording sites relative to standardized anatomical frameworks.
• Viral tracing and expression mapping: Delineate and quantify viral expression patterns and labeled cells across injections and tissue sections.
• Anatomical targeting and circuit mapping: Support precise anatomical targeting and comparative anatomical analyses in rodent models using atlas-based delineations.

Methodology:

Register electrode locations and viral expression patterns to annotated 3D atlas volumes (Waxholm Space Atlas of the Sprague Dawley Rat Brain, Allen Mouse Brain Atlas), visualize data in 2D/3D, generate custom-angle atlas slices, apply free transformations to align tissue sections with atlas slices, reconstruct 3D brain meshes from individual tissue, and delineate multi-injection expression patterns with cell counting.