xnat-ingest 0.12.1

Uploads exported DICOM and raw data to XNAT, parsing metadata from DICOMs

XNAT Ingest

XNAT-Ingest is a toolkit used for sorting data into project/subject/sessions, de-identifying images before uploading them to an XNAT instance. Support for various file formats is provided through the FileFormats package and its extensions (e.g. FileFormats MedImage, FileFormats Siemens,...).

flowchart LR
    Scanner(["Scanner / instrument"]) --> Group["group"]
    Group --> Assign["assign"]
    Assign --> Deidentify["deidentify (optional)"]
    Deidentify --> Upload["upload"]
    Upload --> XNAT[("XNAT")]
    Upload -.-> CheckUpload["check-upload"]

    Extra(["files without\nsorting metadata"]) -.-> Associate["associate (optional)"]
    Assign -.-> Associate
    Associate -.-> Deidentify

Installation

XNAT ingest can be installed as a Python package from PyPI with pip:

$ python3 -m pip install xnat-ingest

Alternatively, a Docker image containing the toolkit can be pulled from docker pull ghcr.io/australian-imaging-service/xnat-ingest:latest

Running

XNAT Ingest has a public API and a command-line interface (CLI), with sub-commands to group, assign, associate, de-identify, and upload imaging sessions to XNAT — either as a one-off run or as a continuously-running service (e.g. via Docker Compose or Kubernetes).

See the full documentation for a hands-on quick start, how-to guides for each part of the pipeline, and the complete CLI/API reference.