Inspiration
Medical students often spend years learning brain anatomy from flat, 2D MRI slices. Many existing 3D tools are costly, complicated, or don’t support teamwork. We wondered: what if studying neuroanatomy could feel as easy and collaborative as working in a shared Google Doc?
What it does
Safe Mind is a free, open-source, web-based 3D brain MRI viewer that combines real-time collaboration with advanced analysis tools.
How we built it
Frontend
HTML, CSS, JavaScript
Three.js for 3D rendering
Raycasting for placing annotations
WebSocket client for collaboration
Backend
Python with FastAPI
WebSockets for live synchronization
NiBabel, NumPy, SciPy, scikit-image (marching cubes)
Pillow for image processing
Vector database for case similarity search
Data Processing
Volumetric processing using the marching cubes algorithm
Multi-resolution mesh generation for performance
Slice extraction and PNG encoding
Tumor segmentation and mesh creation
Deployment
Hosted on Render with GitHub CI/CD
Desktop distribution via PyInstaller
Cross-platform support (Windows, macOS, Linux)
Challenges we ran into
Keeping camera movement, slices, and annotations synchronized without lag or feedback loops
Rendering large volumetric datasets efficiently (256 × 178 × 256 voxels)
Making 3D annotation placement intuitive using raycasting
Balancing mesh quality and real-time performance
Building reliable WebSocket communication for collaboration
Accomplishments that we're proud of
Making this.
What we learned
Designing WebSocket architectures for collaborative apps
3D interaction and raycasting in Three.js
Isosurface extraction using marching cubes
The importance of real-time state syncing in shared tools
Optimizing performance for 3D medical visualization
What's next for Safe Mind
Brain region labeling with anatomical overlays
Support for DICOM files
Mobile-friendly viewer
Expanded AI analysis capabilities
More advanced segmentation tools
PACS system integration
Advanced measurement tools
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