niivue-streamlit 0.2.2b3

A Streamlit component for NiiVue neuroimaging viewer

NiiVue Streamlit Component

A modern Streamlit component for visualizing neuroimaging data using NiiVue, built with TypeScript, Preact, and Vite.

🚀 Quick Start

Simple Installation & Usage

1. Install the component:

   pip install --index-url https://test.pypi.org/simple/ --no-deps niivue-streamlit
   

2. Use in your Streamlit app:

   import streamlit as st
   from niivue_component import niivue_viewer
   
   uploaded_file = st.file_uploader("Choose a NIFTI file", type=["nii", "nii.gz"])
   
   if uploaded_file is not None:
       result = niivue_viewer(
           nifti_data=uploaded_file.getvalue(),
           filename=uploaded_file.name,
           height=700
       )
   
       # Handle click events
       if result:
           st.write(f"Clicked voxel: {result['voxel']}, Value: {result['value']}")
   

✨ Features

• 🎨 Two Component Modes:
  • StyledViewer: Full-featured viewer with interactive menu and controls
  • UnstyledCanvas: Minimal canvas-only viewer for embedding
• 🔄 Multiple View Modes:
  • Axial, Coronal, Sagittal slices
  • 3D render view
  • Multiplanar view with render
• 📊 Advanced Capabilities:
  • Multiple overlay images with custom colormaps
  • Configurable display settings (crosshair, radiological convention, colorbar, interpolation)
  • Bidirectional communication (click events from viewer to Python)
  • DICOM support

📖 Advanced Usage

With Overlays

from niivue_component import niivue_viewer

result = niivue_viewer(
    nifti_data=main_image_bytes,
    filename="brain.nii.gz",
    overlays=[
        {
            "data": overlay_bytes,
            "name": "activation.nii.gz",
            "colormap": "hot",
            "opacity": 0.7
        }
    ],
    view_mode="multiplanar",
    styled=True,
    settings={
        "crosshair": True,
        "radiological": False,
        "colorbar": True,
        "interpolation": True
    },
    height=800
)

Minimal Viewer (No Menu)

# Perfect for embedding in complex layouts
result = niivue_viewer(
    nifti_data=image_bytes,
    filename="scan.nii",
    styled=False,  # Hide menu
    view_mode="axial",
    height=400
)

📚 API Reference

niivue_viewer()

Parameters:

• nifti_data (bytes, optional): Raw NIFTI file data
• filename (str): Displayed filename
• overlays (list[dict], optional): Overlay images list
  • data (bytes): Overlay data
  • name (str): Overlay name
  • colormap (str): Colormap (default: 'red')
  • opacity (float): 0-1 (default: 0.5)
• height (int): Height in pixels (default: 600)
• view_mode (str): 'axial', 'coronal', 'sagittal', '3d', 'multiplanar' (default)
• styled (bool): Show menu (default: True)
• settings (dict, optional):
  • crosshair (bool): default True
  • radiological (bool): default False
  • colorbar (bool): default False
  • interpolation (bool): default True
• key (str, optional): Component key

Returns:

dict or None with click event data:

• type: 'voxel_click'
• voxel: [x, y, z]
• mm: [x, y, z]
• value: float
• filename: str

🛠️ Development

Frontend Development

Built with modern web technologies:

• Vite: Fast build tool
• TypeScript: Type safety
• Preact: Lightweight React
• Tailwind CSS: Styling
• niivue-react: Shared components

cd niivue_component/frontend

# Start dev server (requires backend running)
pnpm dev

# Build for production
pnpm build

Backend Development

Toggle dev/production in __init__.py:

_RELEASE = False  # Dev mode: localhost:3001
_RELEASE = True   # Prod mode: built files

Running Examples

# Simple example
streamlit run app.py

# Advanced example with all features
streamlit run app_advanced.py

📁 Supported Formats

• NIFTI (.nii, .nii.gz)
• DICOM (.dcm)
• MINC (.mnc, .mnc.gz)
• MHA/MHD
• NRRD
• MGH/MGZ

🏗️ Architecture

niivue_component/
├── __init__.py                 # Python API
├── frontend/
│   ├── src/
│   │   ├── components/
│   │   │   ├── StyledViewer.tsx
│   │   │   └── UnstyledCanvas.tsx
│   │   ├── types.ts
│   │   └── utils.ts
│   ├── vite.config.ts
│   └── package.json
└── build/                      # Compiled assets (generated, not in git)

🔧 Building the Component

The build files are not committed to git. To build the component locally:

cd niivue_component/frontend
pnpm install
pnpm build

This generates the build/ directory with compiled assets that are included in the Python package during distribution.

📄 License

BSD-2-Clause

🙏 Credits

Built on top of:

• NiiVue
• Streamlit
• niivue-react