niivue-streamlit 0.0.0.dev38

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
  • Surface mesh rendering (FreeSurfer pial, white, inflated, GIfTI, STL, OBJ, etc.)
  • Mesh overlays (curvature, thickness, annotations)
  • Combined volume + mesh visualization
  • 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
)

With Mesh Surfaces

from niivue_component import niivue_viewer

# Load a FreeSurfer surface mesh
mesh_data = open("lh.pial", "rb").read()

result = niivue_viewer(
    meshes=[{
        "data": mesh_data,
        "name": "lh.pial",
    }],
    view_mode="3d",
    height=700
)

Mesh with Overlays (Curvature, Thickness)

mesh_data = open("lh.pial", "rb").read()
thickness_data = open("lh.thickness", "rb").read()

result = niivue_viewer(
    meshes=[{
        "data": mesh_data,
        "name": "lh.pial",
        "overlays": [{
            "data": thickness_data,
            "name": "lh.thickness",
            "colormap": "redyell",
            "opacity": 0.7
        }]
    }],
    view_mode="3d",
    height=700
)

Volume with Mesh

# Display a volume image alongside a surface mesh
volume_data = open("brain.nii.gz", "rb").read()
mesh_data = open("lh.pial", "rb").read()

result = niivue_viewer(
    nifti_data=volume_data,
    filename="brain.nii.gz",
    meshes=[{
        "data": mesh_data,
        "name": "lh.pial",
    }],
    view_mode="3d",
    height=700
)

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
)

⚡ Performance

Because Streamlit re-runs the whole script whenever a component calls Streamlit.setComponentValue, bidirectional click feedback from the viewer can become a bottleneck: without care, every mouse event re-reads the file, re-base64-encodes the NIfTI, and re-transmits it to the iframe. Three knobs keep the viewer snappy:

1. @st.fragment — wrap the viewer plus the UI that consumes its return value in a fragment. Clicks re-run only the fragment, not the whole page. See app_bidirectional.py.
2. @st.cache_data — cache Path.read_bytes() so the same bytes aren't re-loaded on every re-run. The component wrapper also caches the base64 encoding internally, keyed on the bytes object's identity, so caching your loader transparently skips re-encoding too.
3. update_interval_ms — controls the throttle on click events sent back to Python (default 100 ms). Pass None to disable feedback entirely when the return value isn't used (e.g. app_simple.py, app_overlay.py, app_advanced.py).

Minimal template:

import streamlit as st
from niivue_component import niivue_viewer
from pathlib import Path

@st.cache_data
def load_nifti(path: str) -> bytes:
    return Path(path).read_bytes()

image = load_nifti("brain.nii.gz")

@st.fragment
def viewer():
    result = niivue_viewer(
        nifti_data=image,
        filename="brain.nii.gz",
        key="viewer",
        update_interval_ms=100,  # or None to disable feedback
    )
    if result:
        st.write(result)

viewer()

📚 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)
• meshes (list[dict], optional): Mesh surfaces list
  • data (bytes): Mesh file data
  • name (str): Mesh filename (must include extension, e.g. 'lh.pial', 'brain.gii')
  • overlays (list[dict], optional): Mesh overlays (curvature, thickness, etc.)
    • data (bytes): Overlay data
    • name (str): Overlay filename
    • colormap (str): Colormap (default: 'redyell')
    • opacity (float): 0-1 (default: 0.7)
• 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
• update_interval_ms (int or None): throttle for click events sent back to Python (default: 100 ms). None disables feedback entirely — use it when the return value isn't consumed to avoid any Python round-trip during mouse interaction.
• 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

Dev mode (live reload)

In dev mode, the Python package points to a local Vite dev server instead of built files.

Terminal 1 — start the frontend dev server (port 3001):

pnpm dev

Terminal 2 — run the example app with the dev flag:

NIIVUE_DEV=1 streamlit run app.py

The frontend hot-reloads on changes.

Production mode (built files)

Build the frontend first, then run Streamlit normally:

pnpm build
streamlit run app.py

_RELEASE = True (the default) serves from niivue_component/frontend/build/.

Running Examples

# Simple example
streamlit run app.py

# Advanced example with all features
streamlit run app_advanced.py

📁 Supported Formats

• Volume-based: NIFTI (.nii, .nii.gz), DICOM (.dcm), MINC (.mnc, .mnc.gz), MHA/MHD, NRRD, MGH/MGZ
• Mesh-based: GIfTI (.gii), FreeSurfer (pial, white, inflated), MZ3 (.mz3), STL (.stl), Wavefront OBJ (.obj), PLY (.ply), BrainSuite DFS (.dfs), Legacy VTK (.vtk)
• Mesh Overlays: GIfTI (.gii), CIfTI-2 (.nii), MZ3 (.mz3), FreeSurfer (CURV, ANNOT), SMP, STC
• Tractography: TCK (.tck), TRK (.trk), TRX (.trx), VTK (.vtk)

🏗️ 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 for Distribution

Build files are not committed to git. To prepare the Python package for release:

pnpm build
python -m build

This compiles frontend assets into niivue_component/frontend/build/, which is then bundled into the Python package.

📄 License

BSD-2-Clause

🙏 Credits

Built on top of:

• NiiVue
• Streamlit
• niivue-react