DMC-BrainMap

DMC-BrainMap streamlines whole-brain analysis of anatomical data by preprocessing images, registering them to reference atlases, segmenting anatomical features, and enabling data analysis and visualization.

Key Features:

• Image Preprocessing: Processes histological images after acquisition to prepare them for downstream analysis.
• Atlas Registration: Registers images to reference brain atlases for standardized coordinate mapping.
• Feature Segmentation: Segments different anatomical features including cell bodies, axonal densities, injection sites, optical fibers, and Neuropixels probes.
• Cross-Species Compatibility: Supports histological data from mouse, rat, and zebrafish at different developmental stages.
• Spatial Transcriptomics Integration: Integrates spatial transcriptomics data into the analysis workflow.
• Data Analysis and Visualization: Provides quantitative mapping and visualization of anatomical features.

Scientific Applications:

• Cell Body Mapping: Maps and quantifies cell body distributions across the brain.
• Axonal Density Quantification: Measures and maps axonal densities throughout brain regions.
• Injection Site Localization: Identifies and maps viral injection sites in intact brains.
• Probe Placement Verification: Maps placement of optical fibers and Neuropixels probes relative to anatomical structures.
• Spatial Transcriptomics Analysis: Integrates spatial transcriptomics data with anatomical reference frameworks.
• Circuit Anatomy Studies: Supports mapping of neuronal circuit components for studies linking circuit activity to behavior.

Methodology:

The tool operates as a napari plugin implementing image preprocessing, registration to reference atlases, segmentation of anatomical features, and subsequent data analysis and visualization.