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DICOM Tools

DICOM Tools provides medical imaging anonymization for privacy-compliant handling of DICOM files.

What It Does

  • Anonymize DICOM files — Remove Protected Health Information (PHI)
  • Regenerate UIDs — Create new unique identifiers for studies, series, and instances
  • Remove private tags — Strip manufacturer-specific metadata
  • Export mapping — Save anonymization mapping as CSV for reference

Why It Matters

Medical imaging files (DICOM) contain sensitive patient information. Sharing these files for:

  • Research collaboration
  • Teaching and presentations
  • Second opinions
  • Publications

...requires removing identifiable information to comply with HIPAA, GDPR, and other privacy regulations.

Accessing DICOM Tools

  1. Open HALO Core
  2. Navigate to DICOM Tools in the sidebar
  3. The page displays anonymization options

Anonymization Options

What Gets Anonymized

By default, HIPAA Safe Harbor identifiers are removed:

Category Tags Anonymized
Patient Data Name, ID, Birth Date, Sex, Age, Address, Weight, Phone, Other IDs
Institution Data Name, Address, Referring Physician
Physician Data Performing Physician, Operators
Study Data Study ID, Accession Number, Dates, Times
Series Data Series Date/Time, Acquisition Date/Time

UID Regeneration

When enabled (default), new UIDs are generated for:

  • Study Instance UID
  • Series Instance UID
  • SOP Instance UID
  • Frame of Reference UID

This ensures anonymized files don't link back to original studies.

Private Tags

Private tags are manufacturer-specific and may contain identifying information. They are removed by default.

Using DICOM Tools

Step 1: Upload Files

  1. Click Dateien hochladen
  2. Select DICOM files (.dcm, .dicom, or files without extension)
  3. Multiple files can be uploaded at once

Step 2: Configure Options

Select what to anonymize:

  • UIDs neu generieren — Regenerate unique identifiers (recommended)
  • Private Tags entfernen — Remove manufacturer-specific tags (recommended)
  • Patientendaten — Patient name, ID, birth date, etc.
  • Institutionsdaten — Hospital/clinic information
  • Studiendaten — Study ID, accession number
  • Datumsangaben — All date/time fields

Step 3: Anonymize

  1. Click Anonymisieren
  2. Wait for processing to complete
  3. Review results in the output section

Step 4: Download

  1. Download anonymized files as ZIP
  2. Optionally download the anonymization mapping CSV

Expected Results

After anonymization:

  • All selected tags are cleared or replaced with placeholder values
  • New UIDs are generated (if enabled)
  • Private tags are removed (if enabled)
  • Files are functionally identical for clinical review
  • Files can be shared without exposing patient identity

Anonymization Mapping

The mapping CSV contains:

Column Description
Original Filename Original file name
Anonymized Filename New file name
Original Patient ID Original patient identifier
Anonymized ID New anonymized identifier
Tags Anonymized List of cleared tags
UIDs Regenerated List of regenerated UIDs

Keep this mapping secure — it links anonymized files to original patients.

Auto-Anonymization on Upload

When enabled in configuration, DICOM files uploaded to Sources are automatically anonymized.

Enable in .env:

DICOM_ANONYMIZE_ON_UPLOAD=true

Behavior

  • Files are anonymized before being added to Sources
  • Original files are not stored
  • Mapping is saved for reference

Troubleshooting

"File not recognized as DICOM"

Possible causes:

  • File is not a valid DICOM file
  • File is corrupted
  • Unsupported DICOM format

Try this:

  1. Verify file is a valid DICOM file
  2. Try opening in a DICOM viewer first
  3. Check file integrity

"Anonymization fails"

Possible causes:

  • File is write-protected
  • Missing dependencies
  • Invalid DICOM structure

Try this:

  1. Check file permissions
  2. Verify pydicom is installed
  3. Try a different DICOM file

"Download fails"

Possible causes:

  • Browser blocking download
  • Large file size
  • Disk space issue

Try this:

  1. Enable pop-ups/downloads for the site
  2. Process fewer files at once
  3. Check available disk space

Best Practices

Before Anonymizing

  • Verify files are correct DICOM format
  • Note any critical metadata that may be needed later
  • Consider which tags are necessary for your use case

After Anonymizing

  • Verify anonymized files open correctly
  • Check that clinical utility is preserved
  • Securely store mapping file if patient linkage is needed
  • Delete original files if no longer needed

For Research

  • Document anonymization process for IRB compliance
  • Store mapping separately from anonymized files
  • Consider de-identification beyond HIPAA Safe Harbor if needed

Next Steps