Mouse Head Reference Atlas Framework

Welcome to the Brain Architecture Project’s Mouse Head Reference Atlas Framework. This section provides access to all mouse-related resources.

Reference Atlas

The Mouse Head Reference Atlas Framework provides a standardized approach for mapping and analyzing mouse head anatomy.

Key Features

• High-resolution 3D atlas
• Standardized coordinate system
• Anatomical landmarks
• Cross-sectional views

Available Data Sets

Mouse Whole Head Imaging Data

Comprehensive collection of standardized datasets for mouse brain architecture.

Categories

• Raw Imaging Data
  • Histology images
  • Radiology images
• Processed Data
  • Segmentation maps
  • Registration results
  • Feature maps
  • Co-registered volumes

Registration Framework

Getting Started

Tools and documentation for registering your data with the mouse head reference atlas.

Quick Start

1. Install dependencies
2. Download reference data
3. Prepare your data
4. Run registration

Skeletonization Framework

Getting Started

Tools and documentation for Skeletonizing tracer-injected Datasets.

Quick Start

1. Install dependencies
2. Download reference data
3. Prepare your data
4. Run Skeletonization and Summarization.

View Skeletonization Page

Code Resources

Available Tools

Registration Framework

Tools and utilities for registering your data with our mouse head reference atlas.

• Data preprocessing scripts
• Registration algorithms
• Validation tools

Analysis Tools

Collection of analysis scripts and notebooks.

• Statistical analysis
• Visualization tools
• Data processing pipelines

Data Processing Tools

• segVoxReassign - Tools for remapping Allen Brain Atlas segmentation IDs to manageable ranges
• Feature extraction utilities
• Segmentation helpers
• align-qc - Tools for quality control and clean up 3D reconstruction of nissls, and for performing semi-automatic rigid alignment (registration) using manual point selection and gradient-based optimization.