Metadata-Version: 2.4
Name: asoct-mcd
Version: 0.2.0
Summary: Minuscule Cell Detection in AS-OCT Medical Images
Author: B. Chen
Maintainer: B. Chen
License: MIT
Project-URL: text, https://github.com/joeybyc/MCD
Keywords: medical-imaging,cell-detection,optical-coherence-tomography,computer-vision,deep-learning
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.9
Description-Content-Type: text/markdown
Requires-Dist: numpy>=1.26.3
Requires-Dist: matplotlib>=3.8.2
Requires-Dist: pandas>=2.1.4
Requires-Dist: opencv-python>=4.9.0.80
Requires-Dist: torch>=2.1.2
Requires-Dist: torchvision>=0.16.2
Requires-Dist: scikit-image>=0.22.0
Requires-Dist: scikit-learn>=1.4.0
Requires-Dist: yacs>=0.1.8
Requires-Dist: segment-anything>=1.0
Requires-Dist: tqdm>=4.67.1

# ASOCT-MCD: Minuscule Cell Detection in AS-OCT Images

A Python package for detecting minuscule cells in Anterior Segment Optical Coherence Tomography (AS-OCT) medical images.

## Installation

```bash
pip install asoct-mcd
```

## Basic Usage

```python
from asoct_mcd.pipeline import MCDPipelineBuilder

# Create pipeline with default settings
pipeline = MCDPipelineBuilder().build()

# Detect cells in image
result = pipeline.detect_cells("path/to/image.png")

# Print results
print(f"Detected {result.cell_count} cells")
print(f"Cell locations: {result.cell_locations}")
```

## Custom Configuration

```python
# Using dictionary configuration
config = {
    "threshold": {"lambda_factor": 0.9, "method": "isodata"},
}

pipeline = MCDPipelineBuilder().from_dict(config).build()
result = pipeline.detect_cells("image.png")
```

```python
# Using YAML configuration
pipeline = MCDPipelineBuilder().from_yaml("your_config.yaml").build()
result = pipeline.detect_cells("image.png")
```


## Requirements
- Python >= 3.9
- See requirements.txt for full list

## Citation

arXiv: https://arxiv.org/abs/2503.12249

To cite MCD in publications, please use:

```bibtex
@article{chen2025minuscule,
      title={Minuscule Cell Detection in AS-OCT Images with Progressive Field-of-View Focusing}, 
      author={Boyu Chen, Ameenat L. Solebo, Daqian Shi, Jinge Wu, Paul Taylor},
      year={2025},
      journal={arXiv preprint arXiv:2503.12249}
}

```
## Acknowledgements
Thanks to the support of AWS Doctoral Scholarship in Digital Innovation, awarded through the UCL Centre for Digital Innovation. We thank them for their generous support.
![](readme_images/AWS.png)
![](readme_images/CDI.png)
