grand-challenge-dicom-de-id-procedure 2025.8.5

De-identification procedure that descibes how to de-identify DICOM files

Grand-Challenge DICOM De-Identification Procedure

This repository contains the code that generate the procedure for the Grand-Challenge.org de-identification methods. The procedure describes which action needs to be taken for a DICOM tag in order to be de-identified.

It is based on the DICOM Basic Profile of the Standard DICOM de-identification profile but customized for the use on the Grand-Challenge platform.

More information about de-identification choices can be found in the standard-operation procedure.

Procedure Usage

For JavaScript you can use the ESM + UDM bundles via the npmjs package:

• https://www.npmjs.com/package/@diagnijmegen/rse-grand-challenge-dicom-deid-procedure

The procedure.json has two lookups: firstly by SOPClassUID and secondly by the data element tag. This results in a "default" action that is to be executed for the data element in question. The action can be any of:

Code	Action
"D"	replace with a non-zero length value that may be a dummy value and consistent with the VR
"Z"	replace with a zero length value, or a non-zero length value that may be a dummy value and consistent with the VR
"X"	remove
"K"	keep (unchanged for non-Sequence Attributes, cleaned for Sequences)
"C"	clean, that is replace with values of similar meaning known not to contain identifying information and consistent with the VR
"U"	replace with a non-zero length UID that is internally consistent within a set of Instances
"R"	reject the entire DICOM file

For Python you can use the PyPi package: https://pypi.org/project/grand-challenge-dicom-de-id-procedure/

$ pip install grand-challenge-dicom-de-id-procedure

To load the procedure import it as follows:

from grand_challenge_dicom_de_id_procedure import procedure

# Check the version
print(procedure["version"])

# Get an action for tag (0008,0005) of SOPClassUID "1.2.840.10008.5.1.4.1.1.2" (CT image)
action = procedure["sopClass"]["1.2.840.10008.5.1.4.1.1.2"]["tag"]["(0008,0005)"]["default"]

print(action) # "K"

Procedure Building

First, install uv you should then be able to run the any of the following make commands:

$ make base

Which will create the base procedure, see Action logic below for details.

$ make candidate

Which will merge BASE + MANUAL procedures to generate a CANDIDATE procedure. The MANUAL procedure is a hand-crafted action list for each DICOM tag that is unset in the BASE procedure.

$ make worklist

Which will generate a reStructuredText that describes the tags for which no action has been set in the CANDIDATE procedure.

These will need to be addressed before we can generate the final procedure.

$ VERSION="2025.6.0" make final

Finally, above will run all the earlier make targets (i.e. base, candidate, worklist) and then use the CANDIDATE procedure to build the distributable FINAL procedure Including a VERSION, as specified.

Procedure Release

Calling make final with a VERSION also inserts the version in the relevant Python and NPM package configuration. The actual package(s) release is done via GitHub actions. The steps are:

1. Ensure that main contains the latest version you would like to release
2. Create and publish a release on GitHub, creating a new tag
   • Versioning dated-semver and follows format YYYY.MM.MINOR, where YYYY is the year MM is the month with no-zero padding and MINOR is the version bump within that month (starting at '0'). For instance 2025.2.0.
3. GitHub actions to publish the new package(s) automatically starts when a release is published
4. Once everything is published, the dependency needs to be updated downstream (e.g. in Grand-Challenge)