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dicom
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Extension repository on GitHub
Extension descriptor (YAML)

DuckDB integration with medical imaging data (DICOM - Digital Imaging and Communication in Medicine).

Maintainer(s): nmontesg

Installing and Loading 

INSTALL dicom FROM community;
LOAD dicom;

Example 

INSTALL dicom FROM community;
LOAD dicom;
FROM read_dicom('path/to/dicom_file.dcm');

About dicom

The dicom extension for DuckDB provides functionality to import medical imaging data (DICOM, Digital Imaging and Communication in Medicine) directly into DuckDB. It uses the powerful DCMTK C++ library to read DICOM files and convert them into JSON format.

For full documentation and examples, see the project documentation.

Key functionality:

  • read_dicom() - Table function to import DICOM files directly into DuckDB, including support for local and remote files.
  • DICOM_TAG - Custom type to work with DICOM tags, including conversion to and from VARCHAR.
  • tag_group(), tag_element(), tag_name() - Scalar functions to work with DICOM tags.
  • dicom secret type - Store credentials to establish connection with remote DICOM modalities, such as PACS systems.
  • query_dicom() and retrieve_dicom() - Table functions to query and retrieve DICOM datasets from a remote modalities directly into DuckDB using C-FIND and C-MOVE commands.

Added Functions

function_name function_type description comment examples
query_dicom table Query remote DICOM nodes using C-FIND commands NULL [FROM query_dicom(host='localhost', port=4242, match_keys={'Modality': 'MR'}, retrieve_keys=['StudyInstanceUID']);, FROM query_dicom(secret='my_dicom_conn_secret', qr_level='series', match_keys={'SeriesDate': '20070101'});]
read_dicom table Load DICOM files into DuckDB. The contents of each file are loaded into a row in JSON format. NULL [SELECT * FROM read_dicom('/path/to/dicom_files/');, SELECT * FROM read_dicom('/path/to/dicom_files/', load_pixel_data = true);]
retrieve_dicom table Retrieve DICOM data from remote modalities using C-MOVE commands NULL [FROM retrieve_dicom('1.3.54.24.5…', host='localhost', port=4242, incoming_port=11112, qr_level='study');, FROM retrieve_dicom(['1.95.3…', '1.56.7…'], secret='my_dicom_conn_secret', qr_level='series');]
tag_element scalar Extracts the element of a DICOM tag, as a VARCHAR containing the element in hexadecimal representation. NULL [SELECT tag_element('0008,01DA')]
tag_group scalar Extracts the group of a DICOM tag, as a VARCHAR containing the group in hexadecimal representation. NULL [SELECT tag_group('0008,01DA')]
tag_name scalar Extracts the name of the DICOM tag. If it can't be found, a VARCHAR with format GGGG,EEEE is returned. NULL [SELECT tag_name('0008,0008')]

Overloaded Functions

This extension does not add any function overloads.

Added Types

type_name type_size logical_type type_category internal
DICOM_TAG 0 STRUCT COMPOSITE true

Added Settings

This extension does not add any settings.