Alveoli-counter

This script analyzes alveoli counts in whole mount images. It subsamples multiple areas from each image, counts the alveoli, and performs statistical analysis and visualization.

Requirements

• Python 3.x
• opencv-python
• numpy
• pandas
• scipy
• matplotlib
• seaborn

Installation

Install the required packages using pip:

pip install opencv-python numpy pandas scipy matplotlib seaborn

Usage

To run the script, use the following command:

python analyze_alveoli.py --image_dir <IMAGE_DIRECTORY> --group1 <GROUP1_NAME> --group2 <GROUP2_NAME> --colors <GROUP1_COLOR> <GROUP2_COLOR> [OPTIONS]

Arguments

• --image_dir: Directory containing the images (required).
• --group1: Name of the first comparison group (required).
• --group2: Name of the second comparison group (required).
• --colors: Colors for the groups in the plot (required). Provide two color values (e.g., "#90EE90" "#0000FF").
• --subsample_size: Size of the subsample in pixels (default: 500).
• --subsample_positions: Subsample positions as a list of (x, y) pairs (default: [100, 100, 300, 100, 500, 100]).
• --start_x: Starting x-coordinate for subsampling (default: 100).
• --start_y: Starting y-coordinate for subsampling (default: 100).

Example

To analyze images in the directory path_to_images, with comparison groups CKO and NC, and using colors #90EE90 for CKO and #0000FF for NC, run the following command:

python analyze_alveoli.py --image_dir "Users/johnvusich/Desktop/PD5_wholemounts" --group1 "CKO" --group2 "NC" --colors "#90EE90" "#0000FF"

Output

The script will produce the following outputs:

• alveoli_counts_by_condition.csv: CSV file containing alveoli counts for each sample, grouped by condition.
• summary_statistics_alveoli.csv: CSV file containing summary statistics for each group, including mean count, standard error, and p-value.
• alveoli_counts_publication_quality.png: A publication-quality plot with boxplots and individual points, saved as a PNG file.

Example Outputs

Example of alveoli_counts_by_condition.csv:

Sample,Condition,Alveoli Count
sample1_CKO_PD5.tif,CKO,100
sample2_CKO_PD5.tif,CKO,120
sample1_NC_PD5.tif,NC,90
sample2_NC_PD5.tif,NC,110

Example of summary_statistics_alveoli.csv:

Condition,Mean Count,Standard Error,p-value
CKO,110,10,0.05
NC,100,10,0.05

Plot

The resulting plot alveoli_counts.png will look like this:

License

This project is licensed under the MIT License - see the LICENSE file for details.