RACLAHE_Image_Enhancement_for_CNN_model_segmentation

RACLAHE Quick Start Guide

Prerequisites

• Docker and Docker Compose installed
• Medical imaging files (DICOM .dcm or NIfTI .nii/.nii.gz)

Step 1: Prepare Your Data

Organize your medical images in folders:

input/
├── patient001/
│   ├── slice001.dcm
│   ├── slice002.dcm
│   └── ...
├── patient002/
│   └── scan.nii.gz
└── ...

Each patient folder should contain either:

• Multiple DICOM files (one per slice), OR
• A single NIfTI file

Step 2: Run with Docker Compose

# Clone the repository
git clone <repository-url>
cd RACLAHE_Image_Enhancement_for_CNN_model_segmentation

# Create directories
mkdir -p input output shared

# Copy your patient data into input/
cp -r /path/to/your/patients/* input/

# Run processing
docker-compose up --build

Step 3: Get Results

Enhanced images will be saved in:

output/RACLAHE OUTPUT/
├── patient001/
│   ├── image_1.dcm
│   ├── image_2.dcm
│   └── ...
└── patient002/
    └── patient002.nii.gz

---

Alternative: Run with Docker (without Compose)

# Build image
docker build -t raclage:3.0 .

# Run with volumes
docker run \
  -v $(pwd)/input:/home/ds/datasets:ro \
  -v $(pwd)/output:/home/ds/persistent-home \
  raclage:3.0

---

EUCAIM Platform

On EUCAIM, volumes are automatically mounted:

• /home/ds/datasets → Your input data (read-only)
• /home/ds/persistent-home → Your output directory
• /home/ds/persistent-shared-folder → Shared storage

Simply deploy the image and it will process all patients in the datasets directory.

---

Configuration

Override paths using environment variables:

docker run \
  -e INPUT_DIR=/custom/input \
  -e OUTPUT_DIR=/custom/output \
  -v $(pwd)/input:/custom/input:ro \
  -v $(pwd)/output:/custom/output \
  raclage:3.0

---

Troubleshooting

No output generated

• Check that input folders contain valid DICOM or NIfTI files
• Look at logs: docker-compose logs

Permission errors

• Ensure input/output directories are writable
• Container runs as user 1000:1000

Processing fails

• Check file format (only .dcm, .nii, .nii.gz supported)
• Verify each patient folder contains only one type (DICOM or NIfTI)
• Review logs for specific error messages

---

Support

For issues or questions:

• Review the main README.md
• Contact: dimzaridis@gmail.com
• Paper: https://doi.org/10.1038/s41598-023-27671-8

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