A methodological pipeline for serial-section imaging and tissue realignment for whole-brain functional and...

Area of Science:

• Neuroscience
• Computational Biology
• Systems Neuroscience

Background:

• Understanding cognition and behavior requires large-scale neural population assessment.
• Neural connectivity patterns are crucial for studying brain function after injury or disease.

Purpose of the Study:

• To present a novel analysis platform for large-scale functional and neuroanatomical connectivity in rodents.
• To enable semi-automated, quantitative whole-brain assessment of neural function and connection.

Main Methods:

• Utilized retrograde tracers and behavioral tests to drive immediate-early gene expression.
• Developed an automated analysis pipeline using open-source and custom platforms.
• Implemented semi-automated segmentation, co-registration, and 3-D reconstruction of neural data.

Main Results:

• Generated a 3-D representation of neural tracer distribution throughout the entire brain.
• Successfully segmented neuronal boundaries and co-registered their positions.
• Enabled quantitative analysis of whole-brain connectivity in a flexible manner.

Conclusions:

• The open-source toolkit facilitates 3-D visualization and quantification of whole-brain data.
• Provides a framework for integrating user-specific analyses and methodologies.
• Offers a flexible platform for various whole-brain analyses, including activation and disease markers.