ZooProcess Library

A Python library meant at reproducing as exactly as possible the behavior of ZooProcess v8.X, a tool for processing Zooscan generated images.

Features

• Scanner background and plain images processing
• Background removal from plain image
• Image segmentation, AKA ROIs extraction from scanned images
• ROIs features generation
• Utility classes for legacy filesystem usage

Installation

You can install the package directly from a GitHub release. It is advised to use a specific version release, not the main branch which might be unstable.

pip install https://github.com/ecotaxa/ZooProcess-lib/archive/refs/tags/v0.6.0.tar.gz

Or download the release tarball and install locally:

# Download the release
wget https://github.com/ecotaxa/ZooProcess-lib/archive/refs/tags/v0.6.0.tar.gz
# Extract the archive
tar -xzf v0.6.0.tar.gz
# Navigate to the extracted directory
cd ZooProcess-lib-0.6.0
# Install the package
pip install -e .

In requirements.txt it should look like:

ZooProcess-lib @ https://github.com/ecotaxa/ZooProcess-lib/archive/refs/tags/v0.6.0.tar.gz

Requirements

• Python 3.10 or higher
• Dependencies:
  • numpy
  • scipy
  • opencv-python
  • pillow

Usage

For complete detailed examples, please see the tests directory, especially test_vignetter.py

Development

Running Tests

Note: You should install manually 'gdown' package before running tests. It's used to download big example TIFF files from a public GDrive folder.

cd tests
python -m pytest --ignore UNUSED/

License

See the LICENSE file for details.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.