This is an image analysis project. 

The aim is to identify blobs in the images stored in the `data/raw/` directory. 
First run the "process_images" script which produced some intermediate files stored in `data/processed/` directory.
Then run the "analyse_images" script to produce the final output files, stored in `data/results/` directory.

Data organisation is summarized below - see file tree.

.
├── data
│   ├── processed
│   │   ├── 003003-11th-October-image4_processed.npy
│   │   ├── 003003-2024-10-11-image1_processed.npy
│   │   ├── 003003-25_10_2024 image10_processed.npy
│   │   ├── 003003-25-10-2024-image6_processed.npy
│   │   ├── 003003-25_10_2024-image7_processed.npy
│   │   ├── 003003-25_10_2024-image8_processed.npy
│   │   ├── 003003-25_10_2024-image9_processed.npy
│   │   ├── 003003_october_2024_image2_processed.npy
│   │   ├── 003003_october_2024_image3_processed.npy
│   │   └── 003003_October_2024_image5_processed.npy
│   ├── raw
│   │   ├── 003003-11th-October-image4.tif
│   │   ├── 003003-2024-10-11-image1.tif
│   │   ├── 003003-25_10_2024 image10.tif
│   │   ├── 003003-25-10-2024-image6.tif
│   │   ├── 003003-25_10_2024-image7.tif
│   │   ├── 003003-25_10_2024-image8.tif
│   │   ├── 003003-25_10_2024-image9.tif
│   │   ├── 003003_october_2024_image2.tif
│   │   ├── 003003_october_2024_image3.tif
│   │   └── 003003_October_2024_image5.tif
│   └── results
│       ├── 003003-11th-October-image4_processed_blob_centroids.png
│       ├── 003003-2024-10-11-image1_processed_blob_centroids.png
│       ├── 003003-25_10_2024 image10_processed_blob_centroids.png
│       ├── 003003-25-10-2024-image6_processed_blob_centroids.png
│       ├── 003003-25_10_2024-image7_processed_blob_centroids.png
│       ├── 003003-25_10_2024-image8_processed_blob_centroids.png
│       ├── 003003-25_10_2024-image9_processed_blob_centroids.png
│       ├── 003003_october_2024_image2_processed_blob_centroids.png
│       ├── 003003_october_2024_image3_processed_blob_centroids.png
│       ├── 003003_October_2024_image5_processed_blob_centroids.png
│       └── all_image_stats.csv
├── README
└── scripts
    ├── analyse_images Jan 2025.py
    ├── analyse_images_NEW.py
    ├── analyse_images.sh
    ├── counting_objects.ipynb
    ├── process_images.py
    └── process_images.sh


N.B. you will need to install the "imagecodecs" package.

The `scripts/` directory contains all the scripts to analyse the data.