XNAT Ingest
XNAT-Ingest is a collection of tools to sort, label, de-identify data and upload them to an XNAT repository. Support for various file types 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)"]
Group -.-> Associate
Associate -.-> Assign
Installation
A Docker image containing the toolkit can be pulled from the GitHub Container Registry and entrypoint of the image is the xnat-ingest CLI so commands can be run by the form
docker run ghcr.io/australian-imaging-service/xnat-ingest:latest <command-name> <arg1> <arg2> ... --opt1 <opt1> ...
Alternatively, XNAT ingest can be installed as a Python package from PyPI with pip:
$ python3 -m pip install xnat-ingest
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.
1 maintainer
Metadata
1 maintainer
Release files for xnat-ingest 0.16.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| xnat_ingest-0.16.1.tar.gz | 191.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| xnat_ingest-0.16.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 425.7 kB
Release files / xnat_ingest-0.16.1.tar.gz
| Download URL | xnat_ingest-0.16.1.tar.gz |
|---|---|
| Size | 191.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / xnat_ingest-0.16.1-py3-none-any.whl
| Download URL | xnat_ingest-0.16.1-py3-none-any.whl |
|---|---|
| Size | 234.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
