Visualize Physarum Petri Dish Detection
Run this script
uv run https://atrium.kyleharrington.com/laboratory/visualize_dish_detection/main.py
Command Line Arguments
--image_path
(str)
--output_path
(str)
Path to save visualization image
--show_plot
(bool)
Whether to display the plot
Default: True
--margin_factor
(float)
Margin factor to leave from edges (0-0.2)
Default: 0.03
--manual_rows
(int)
Number of rows in dish layout
Default: 3
--manual_cols
(int)
Number of columns in dish layout
Default: 2
--downsample
(float)
Downsample ratio for processing (0.1-1.0)
Default: 0.5
--image_path
(str)
--dish_index
(int)
Index of the dish to analyze (0-5)
Default: 0
--rows
(int)
Number of rows in dish layout
Default: 3
--cols
(int)
Number of columns in dish layout
Default: 2
--output_path
(str)
Path to save comparison image
--input_dir
(str)
--pattern
(str)
File pattern to match
Default: *.png
--rows
(int)
Number of rows in dish layout
Default: 3
--cols
(int)
Number of columns in dish layout
Default: 2
--margin_factor
(float)
Margin factor for detection
Default: 0.03
--downsample
(float)
Downsample ratio for processing
Default: 0.5
--output_dir
(str)
Directory to save visualizations
Dependencies
- numpy>=1.24.0
- pillow>=10.0.0
- typer>=0.9.0
- opencv-python>=4.8.0
- scikit-image>=0.21.0
- matplotlib>=3.7.0