DMC-BrainMap is an open-source, end-to-end tool for multi-feature brain mapping in different species

Area of Science:

• Neuroscience
• Bioinformatics
• Computational Biology

Background:

• Accurate anatomical mapping is crucial for understanding brain structure and function.
• Current methods for processing and analyzing neuroanatomical data can be complex and time-consuming, requiring significant programming expertise.
• There is a need for accessible, streamlined tools to facilitate whole-brain analysis in neuroscience research.

Purpose of the Study:

• To introduce DMC-BrainMap, an open-source napari plugin designed for user-friendly, streamlined processing and whole-brain analysis of anatomical data.
• To provide a comprehensive solution for post-image acquisition steps, including preprocessing, registration, segmentation, and analysis/visualization.
• To enhance rigor, reproducibility, and data sharing in neuroscientific research involving animal models.

Main Methods:

• Development of DMC-BrainMap as an open-source napari plugin.
• Implementation of core functionalities covering image preprocessing, atlas registration, anatomical feature segmentation, and data analysis/visualization.
• Application to diverse histological data from multiple model organisms (mice, rats, zebrafish) and developmental stages.

Main Results:

• Demonstrated utility of DMC-BrainMap for mapping and quantifying various features including cell bodies, axonal densities, injection sites, and optical fiber/Neuropixels tracts.
• Successful application to single-cell spatial transcriptomics and neuron morphology data.
• Validation across different species and developmental stages, highlighting the plugin's versatility.

Conclusions:

• DMC-BrainMap offers a powerful, yet easy-to-use, solution for complex neuroanatomical data analysis.
• The plugin eliminates the need for user programming, thereby increasing accessibility and adoption in the neuroscience community.
• DMC-BrainMap significantly contributes to advancing reproducible and shareable neuroscientific research using animal models.