cabana 0.1.1

Collagen fibre analyser for quantifying collagen fibre architecture in IHC and fluorescence microscopy images.

CABANA (CollAgen FiBre ANAlyzer) is a comprehensive toolkit for analyzing collagen fibre architecture in immunohistochemistry (IHC) and fluorescence microscopy images. It provides:

• Automated detection and quantification of collagen fibres
• Analysis of fibre orientation, length, and thickness
• Gap analysis for inter-fibre and intra-fibre spaces
• Interactive parameter optimization interface
• Batch processing for large datasets

CABANA combines advanced computer vision algorithms with an intuitive user interface, making it accessible to researchers without extensive programming experience while providing detailed quantitative data for comprehensive analysis of collagen architecture.

System Requirements

• Processor (CPU): Intel Core i7, AMD Ryzen 7, or higher recommended
• Memory (RAM): Minimum 16 GB, 32 GB recommended
• GPU: NVIDIA GeForce GTX/RTX series with at least 10 GB VRAM recommended
• Python: 3.8 or newer

Quick Installation

Install CABANA using pip:

pip install -U cabana

or install the latest version on GitHub:

pip install git+https://github.com/lxfhfut/Cabana.git

After installation, you can launch the CABANA GUI by running:

python -m cabana

Alternatively, you can import CABANA in your Python code for customized analysis (see examples in Tutorials):

import cabana

Documentation

Comprehensive documentation is available at: https://cabana.readthedocs.io/en/latest/

Tutorials

We provide an interactive Jupyter notebook tutorial to help you get started: CABANA Tutorial

Citation

If you use CABANA in your research, please cite:

License

CABANA is released under the MIT License.

Contact

For questions and support, please contact:

• Xufeng Lin - [e-mail]
• Astrid Magenau - [e-mail]