Example Notebooks

Jupyter notebooks demonstrating how to use the KymFlow Python API.

Available Notebooks

Notebooks are located in the notebooks/ directory of the repository:

• display_one_kym.py - Example script for displaying a single kymograph
• quality_control.ipynb - Quality control workflow

Running Notebooks

1. Install notebook dependencies:

   pip install kymflow[notebook]
   

2. Launch Jupyter Lab:

   jupyter lab --notebook-dir notebooks
   

3. Open and run the notebooks to see examples of:

4. Loading kymograph files
5. Accessing metadata
6. Running flow analysis
7. Visualizing results

Example Code

from kymflow_core.kym_file import KymFile

# Load a kymograph file
kym = KymFile("path/to/file.tif", load_image=False)

# Access metadata
print(f"Duration: {kym.duration_seconds} seconds")
print(f"Pixels per line: {kym.pixels_per_line}")

# Load image when needed
image = kym.ensure_image_loaded()

# Run analysis
kym.analyze_flow(window_size=16)

# Save results
kym.save_analysis()