spine-harmony-agent

DICOM Export Tool

Convert user-owned DICOM/MRI files into high-resolution PNG review images and optional contact sheets.

Install dependencies

python -m pip install pydicom pillow numpy

Basic conversion

python tools/dicom-export/dicom_export.py /path/to/DICOM_FOLDER /path/to/output-folder

The tool recursively scans the input folder, reads DICOM files, applies DICOM rescale/windowing where available, and writes PNG files grouped by series.

Create a contact sheet

python tools/dicom-export/dicom_export.py /path/to/DICOM_FOLDER /path/to/output-folder --contact-sheet

Outputs:

output-folder/
├── series-001_.../
│   ├── series-001_instance-0001_....png
│   └── ...
├── export_manifest.csv
└── contact_sheet.jpg

What this tool does

• Reads DICOM files using pydicom.
• Applies rescale slope/intercept.
• Uses DICOM window center/width when available.
• Falls back to robust percentile scaling when window fields are missing.
• Handles MONOCHROME1 inversion.
• Exports high-resolution PNG images without downsampling.
• Optionally creates a JPEG contact sheet for quick review.

What this tool does not do

• It does not diagnose.
• It does not interpret MRI findings.
• It does not validate measurements.
• It does not segment anatomy.
• It does not remove all possible identifiers from source DICOM files.
• It does not make outputs safe to publish.

Treat raw DICOM files, exported PNGs, contact sheets, and manifests as sensitive medical data.

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