Vision

Application to work with images and other visual information.
The app contains a lot of plugins to preprocess and analyze segmentation results. Necessary plugins can be enabled/disabled using plugin manager.

Project handling:

• Folder-based projects: Load layers from a directory structure (e.g., images/, masks/) without a project file.
• Project files (planned): Save and load complete layer state in two ways:
  • Referenced: Stores only links to your original files.
  • Self-contained: Embeds all data inside the project file.

For architecture and design principles, see ARCHITECTURE.md.

Python Environment

python 3.11

pip install pyside6 ruamel-yaml numpy opencv-python scikit-image scipy sortedcontainers onnxruntime-gpu pandas nibabel pydicom slideio tifffile pytest cx-freeze

Mandatory Dependencies

• Python 3.10+
• PySide6 6.5+: Python bindings for Qt, used for GUI and signal/slot mechanism.
• ruamel-yaml 0.17+: YAML parser and emitter for config files.

Common Optional Dependencies

• numpy: Stores and processes image data.
• opencv-python: Provides optimized image processing algorithms.
• scikit-image: Wide range of image processing algorithms not in opencv-python (most often opencv-python methods have better performance).
• scipy: Mostly for data interpolation.
• sortedcontainers: Sorted collections library.

Specialized Dependencies

• Neural Network Inference

  • onnxruntime-gpu: Infers neural network models on GPUs and CPUs.

• Data Analysis and File Format Handling

  • pandas: Data analysis tool.
  • nibabel: Reads NIfTI files.
  • pydicom: Reads DICOM files.
  • slideio: Reads high-resolution medical slides (Whole Slide Imaging).
  • tifffile: Manages tiled multi-resolution (pyramid) TIFF files.

• Testing

  • pytest: Testing framework.

• Build and Packaging

  • cx-freeze: Creates standalone executables and installers.

Running the Application from Source

To run the application, configure your IDE to recognize the src directory as the source root.
Then run bsmu/vision/app/main.py:

PyCharm

1. Right-click on the src folder.
2. Select Mark Directory as -> Sources Root.
3. Right-click on bsmu/vision/app/main.py and select Run.

VS Code

Use predefined configurations in the launch.json file, located in the .vscode folder:

1. Open the Run and Debug view by clicking on the Run and Debug icon in the Activity Bar (or use the shortcut Ctrl+Shift+D).
2. In the dropdown menu at the top of the Run and Debug view, select the configuration: Python: Run main.py.
3. Click the green play button (Start Debugging) next to the dropdown menu to run the selected configuration. If you want to run without debugging, use the shortcut Ctrl+F5.

Building the .exe

Run the scripts/build.py script with the argument build:

PyCharm

1. Right-click on the scripts/build.py script and select Modify Run Configuration....
2. In the Script parameters field, enter: build.
3. Right-click on the scripts/build.py script again and select Run.

VS Code

1. In the Run and Debug view, select the configuration: Python: Run build.py.
2. Run the selected configuration (Ctrl+F5 - without debugging; F5 - with debugging).

Contributing

For guidelines on contributing, please see CONTRIBUTING.md.