AQUILA

AQUILA is a Python application with a Qt-based GUI for microscopy foci analysis and visualization.

Features

• Pipeline Functionalities:

  • Specify input directory for reading files
  • Specify output directory for image annotations and summary dataframe/plots

• Utilities:

  • Robust image reading for different file types.
  • Difference of Gaussians (DoG) image blurring for robust foci detectiion.
  • Nuclear segmentation.
  • Output plot for integrated data analysis.

• Adjustable Parameters:

  • Foci Detection
    • DoG sigma values: Controls image blurring and foci calling (Sigma A subtracted from Sigma B).
    • Prominence: Sets minimum intensity to consider calling a focus.
  • Nuclear Segmentation
    • Min and Max Area: Sets pixel size of nuclei to exclude undesired nuclei or clumps.
    • DAPI Foreground: Aesthetic preference for nuclear segmentation (light nuclei on dark background or dark nuclei on light background)
    • Sigma Blur: Blurs nuclei to make threhsolding more stable and ensure proper nucleus segmentation.
    • Seed radius: Controls nuclear erosion and segmentation during thresholding.
  • Advanced
    • Maxima Sigma Smoothing: Applies blur to image after DoG for robust foci detection.
    • Minimum Distance Between Maxima: Sets minimum distance between detected foci to avoid counting the same focus twice.
    • Extensions: Specifies what image extensions should be considered when extracting images from the directory.

Files

• aquila_main.py — The main entry point for the GUI application.

  • Launches the main window (AquilaWindow) and menu screen.
  • Handles user interaction via Qt widgets.

• aquila_utils.py — Utility functions and classes for image processing, file handling, and plotting.

  • Robust image reading (TIFF, PNG, JPEG, etc.).
  • Helper functions.
  • Uses NumPy, pandas, OpenCV, scipy and scikit-image libraries for analysis. Matplotlib and seaborn are used for plotting functions.

• AquilaWindow.py — Harbors AquilaWindow class

• MenuScreen.py — Harbors MenuScreen class

Requirements

• Python 3.12+
• PySide6
• PyObjC (Optional, for loading icon on Mac only)
• numpy
• pandas
• tifffile
• opencv-python
• Pillow
• scikit-image
• scipy
• matplotlib
• seaborn

Install dependencies with:

pip install -r requirements.txt

Usage

1. Run the main application from the downloaded directory with AquilaWindow.py, MenuScreen.py, aquila_main.py and aquila_utils.py:

sh python aquila_main.py

2. The GUI will launch with a menu and options to run analysis.

License

See LICENSE for details.

Contributing

If you would like to contribute to this project, feel free to open an issue or submit a pull request. All suggestions and improvements are welcome.

Contact

For any inquiries, you can reach out to the developer at: pguerra@unc.edu