SMART

SMART performs semi-manual registration and segmentation of intact mouse brain light-sheet fluorescence microscopy (LSFM) datasets to map cellular signals to anatomical reference templates, building upon the WholeBrain framework.

Key Features:

• Semi-automated registration: Provides semi-manual alignment of LSFM datasets along the anterior-posterior (AP) axis by combining automated segmentation with user-guided registration.
• Flexible image handling: Supports registration of whole brains, partial brains, selected images, and specific regions of interest.
• Compatibility with coronal section-based analyses: Enables integration and comparison with traditional serial coronal section datasets and analyses.
• Streamlined volumetric workflow: Implements steps for aligning, registering, and segmenting volumetric LSFM datasets.
• Robustness to incomplete data: Addresses damaged or partially imaged brains by maintaining registration and segmentation accuracy on incomplete datasets.
• Addresses voxel-based method limitations: Reduces dependence on fully automated voxel-based approaches that typically demand high computational resources and complex implementation.

Scientific Applications:

• Immediate early gene (IEG) mapping: Facilitates brain-wide mapping of IEG expression (e.g., Fos) in intact mouse brains imaged by LSFM.
• Region assignment of labeled cells: Enables assignment of IEG-positive neurons or other labeled cells to known anatomical regions of interest (ROIs).
• Brain-wide activity pattern analysis: Supports identification and comparison of brain-wide neuronal activation patterns associated with behavioral paradigms.

Methodology:

SMART uses a semi-manual alignment process that combines automated segmentation with user-guided registration to align, register, and segment volumetric LSFM datasets along the anterior-posterior axis.