GUI Application

BM3DORNL includes a standalone GUI application for interactive ring artifact removal from tomography data.

Installation

# Install with the main package
pip install bm3dornl[gui]

# Or install separately
pip install bm3dornl-gui

Launching

bm3dornl-gui

Features

Data Loading

  • Load HDF5 files with interactive tree browser for dataset selection

  • Load TIFF files (single images or stacks)

  • Support for 2D and 3D datasets

  • Automatic data type detection

Visualization

  • Interactive slice viewer with scroll-wheel navigation

  • Real-time histogram display

  • Adjustable window/level (contrast) controls

  • Side-by-side comparison of original and processed images

Processing

  • Real-time parameter adjustment

  • Support for both generic and streak modes

  • Live preview of denoising results

ROI Selection

  • Shift+drag to select a region of interest

  • Histogram updates to show ROI statistics

  • Useful for evaluating local noise characteristics

Export

  • Export processed data to TIFF format

  • Export to HDF5 format

  • Batch export of full stacks

Keyboard Shortcuts

Shortcut

Action

Scroll wheel

Navigate through slices (3D data) or zoom

Drag

Pan image

Shift + Drag

Select ROI for histogram

Workflow

  1. Load Data: Click “Open” and select an HDF5 or TIFF file. For HDF5, use the tree browser to select a dataset.

  2. Adjust View: Use window/level controls or scroll to navigate through slices.

  3. Select Parameters: Adjust denoising parameters in the control panel:

    • Mode: streak for ring artifacts, generic for random noise

    • Sigma: Start low (0.02-0.05) and increase as needed

    • Other parameters: Usually defaults work well

  4. Process: Click “Process” to apply denoising. Compare with original using the split view.

  5. Evaluate: Use ROI selection (Shift+drag) to check noise statistics in specific regions.

  6. Export: Save processed data to TIFF or HDF5 format.

Tips

  • Start with defaults: The default parameters work well for most cases.

  • Use streak mode: For ring artifacts in sinograms, always use mode="streak".

  • Check the histogram: The histogram should narrow after denoising, indicating reduced noise.

  • Use ROI selection: Select flat regions to evaluate noise reduction without signal interference.

  • Monitor the difference: The removed signal should show primarily vertical streaks (for streak mode), not horizontal structure.