ABCA4 FAF Analysis

Analysis pipeline for FAF (Fundus Autofluorescence) images related to ABCA4.

graph TD
    FafDenoising["FafDenoising"]
    FafRecalibration["FafRecalibration"]
    FafFoveaDisc["FafFoveaDisc"]
    FafAutoBg["FafAutoBg"]
    FafVasculature["FafVasculature"]
    FafInnerMask["FafInnerMask"]
    FafOuterMask["FafOuterMask"]
    FafBgHistogram["FafBgHistogram"]
    FafROIHistogram["FafROIHistogram"]
    FafPixelScore["FafPixelScore"]

    FafDenoising --> FafRecalibration
    FafRecalibration --> FafFoveaDisc
    FafRecalibration --> FafVasculature
    FafFoveaDisc --> FafInnerMask
    FafFoveaDisc --> FafOuterMask
    FafAutoBg --> FafBgHistogram
    FafVasculature --> FafInnerMask
    FafVasculature --> FafOuterMask
    FafInnerMask --> FafROIHistogram
    FafOuterMask --> FafAutoBg
    FafOuterMask --> FafBgHistogram
    FafBgHistogram --> FafPixelScore
    FafROIHistogram --> FafPixelScore

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Getting Started

This project requires Python 3.13 or higher. We recommend using uv for dependency management and virutalenv (or venv) for isolation.

Installation

1. Clone the repository:

   git clone <repository_url>
   cd ABCA4-faf

2. Create a virtual environment: Using standard venv:

   python3.13 -m venv venv
   source ./venv/bin/activate

   Or using uv (recommended):

   uv venv --python 3.13
   source ./venv/bin/activate

3. Install dependencies: This project uses pyproject.toml. You can install the project in editable mode with its dependencies using uv or pip.

   Using uv (faster):

   # If using uv sync (with uv.lock)
   uv sync
   
   # Or strict pip install
   uv pip install -e .

   Using pip:

   pip install -e .

A note on installing uv

To avoid the scary message from snap:

error: This revision of snap "astral-uv" was published using classic confinement and thus may
       perform arbitrary system changes outside of the security sandbox that snaps are usually
       confined to, which may put your system at risk.

use

curl -LsSf https://astral.sh/uv/install.sh | sh

This will install uv in $HOME/.local/bin

Documentation

• Pipeline Execution: Detailed instructions on how to start the pipeline, run the CLI, and understand the workflow.
• Individual Scripts: A brief reference for the individual scripts and modules located in the src directory.

Pipeline Quick Start

Once installed, you can use the pipeline command:

# List available jobs
pipeline list-jobs

# Run pipeline on an image
pipeline run /path/to/image.tiff