imgnet CLI

imgnet

IMGNET CLI - toolkit for facilitating access to standardized medical imaging datasets for cancer research and clinical AI applications.

Usage:

imgnet [OPTIONS] COMMAND [ARGS]...

Options:

Name	Type	Description	Default
--quiet, -q	boolean	Suppress all logging except errors, overrides verbosity options.	False
--verbose, -v	integer range (0 and above)	Increase verbosity of logging, overrides environment variable. (0-3: ERROR, WARNING, INFO, DEBUG).	0
--version	boolean	Show the version and exit.	False
-h, --help	boolean	Show this message and exit.	False

Subcommands

• collections: Inspect indexed collections.
• download: Download instances from a manifest file or a query token.
• query: Query indexed datasets and save selected series for downstream use.
• update-index: Update the indexed datasets: download from Hugging Face.

collections

Inspect indexed collections.

Usage:

imgnet collections [OPTIONS] COMMAND [ARGS]...

Options:

Name	Type	Description	Default
--help, -h	boolean	Show this message and exit.	False

Subcommands

• info: Show basic metadata for a collection; use --tags for queryable columns.
• overview: Show a comprehensive visual overview of the full index.
• summary: Display the collections summary.

info

Show basic metadata for a collection; use --tags for queryable columns.

Usage:

imgnet collections info [OPTIONS] COLLECTION_NAME

Options:

Name	Type	Description	Default
--help, -h	boolean	Show this message and exit.	False
--tags, -t	boolean	Include supported query tags per modality (for building rules).	False
--json	boolean	Print metadata as JSON instead of a table.	False

overview

Show a comprehensive visual overview of the full index.

Usage:

imgnet collections overview [OPTIONS]

Options:

Name	Type	Description	Default
--help, -h	boolean	Show this message and exit.	False
--update, -u	boolean	Rebuild the collections summary before generating the overview.	False

summary

Display the collections summary.

Usage:

imgnet collections summary [OPTIONS]

Options:

Name	Type	Description	Default
--help, -h	boolean	Show this message and exit.	False
--update, -u	boolean	Update the collections summary.	False

download

Download instances from a manifest file or a query token.

MANIFEST_OR_TOKEN: Path to a manifest CSV, or a query token from imgnet query.

Usage:

imgnet download [OPTIONS] [MANIFEST_OR_TOKEN]

Options:

Name	Type	Description	Default
--output-dir, -o	directory	Path to the output directory.	None
--process, -p	boolean	Process all dicom files in the output directory using imgtools.	False
--delete-srcdata	boolean	Delete the source data after processing.	False
--help	boolean	Show this message and exit.	False

query

Query indexed datasets and save selected series for downstream use.

Saves query_results.csv, valid_query.json, and valid_query_schema.json to the output directory. Pipe the output into imgnet download to retrieve the matched series.

Usage:

imgnet query [OPTIONS]

Options:

Name	Type	Description	Default
--output-dir, -o	directory	Path to the output directory.	None
--input-path, -i	file	Path to a valid query json.	None
--collections, -c	text	List of collections to query, or 'all' to query every collection (example: -c collection1 collection2)	['all']
--modalities, -m	text	List of modality queries (example: -m CT,RTSTRUCT CT,SEG)	['all']
--file_type, -ft	choice (all | dicom | nifti)	Restrict query to a specific file type (e.g. 'dicom', 'nifti'). Use 'all' (default) for no restriction.	None
--rules, -r	text	JSON string of filter rules.	None
--help	boolean	Show this message and exit.	False

update-index

Update the indexed datasets: download from Hugging Face.

Examples:

imgnet update-index --path /custom/indexed_datasets

Usage:

imgnet update-index [OPTIONS]

Options:

Name	Type	Description	Default
--path, -p	path	Path to the indexed_datasets directory. Defaults to $IMGNET_INDEX_DIR/indexed_datasets or platform user data dir.	None
--help	boolean	Show this message and exit.	False