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CLI Reference

Command Line Interface (CLI) of Aignostics Python SDK providing access to Aignostics Platform.

Usage:

$ aignostics [OPTIONS] COMMAND [ARGS]...

Options:

  • --install-completion: Install completion for the current shell.
  • --show-completion: Show completion for the current shell, to copy it or customize the installation.
  • --help: Show this message and exit.

🔬 Aignostics Python SDK v1.2.0 - built with love in Berlin 🐻 // Python v3.14.1

Commands:

  • launchpad: Open Aignostics Launchpad, the graphical...
  • notebook: Run Python notebook server based on Marimo.
  • mcp: MCP (Model Context Protocol) server for AI...
  • application: List and inspect applications on...
  • bucket: Operations on cloud bucket on Aignostics...
  • dataset: Download datasets from National Institute...
  • sdk: Platform operations such as dumping the...
  • user: User operations such as login, logout and...
  • qupath: Interact with QuPath application.
  • system: Determine health, info and further...
  • wsi: Operations on whole slide images.

aignostics launchpad

Open Aignostics Launchpad, the graphical user interface of the Aignostics Platform.

Usage:

$ aignostics launchpad [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics notebook

Run Python notebook server based on Marimo.

Usage:

$ aignostics notebook [OPTIONS] [NOTEBOOK]

Arguments:

  • [NOTEBOOK]: Path to the notebook file to run. If not provided, a default notebook will be used. [default: (<sdk-install-dir>/notebook/_notebook.py)]

Options:

  • --host TEXT: Host to bind the server to [default: 127.0.0.1]
  • --port INTEGER: Port to bind the server to [default: 8001]
  • --override-if-exists / --no-override-if-exists: Override the notebook in the user data directory if it already exists. [default: no-override-if-exists]
  • --help: Show this message and exit.

aignostics mcp

MCP (Model Context Protocol) server for AI agent integration.

Usage:

$ aignostics mcp [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • run: Run the MCP server.
  • list-tools: List all available MCP tools.

aignostics mcp run

Run the MCP server.

Starts an MCP server using stdio transport that exposes SDK functionality to AI agents. The server automatically discovers and mounts tools from the SDK and any installed plugins.

Examples: uv run aignostics mcp run

Usage:

$ aignostics mcp run [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics mcp list-tools

List all available MCP tools.

Shows all tools available in the MCP server, including tools from the SDK and any installed plugins. Each tool is displayed with its name and description.

Examples: uv run aignostics mcp list-tools

Usage:

$ aignostics mcp list-tools [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics application

List and inspect applications on Aignostics Platform.

Usage:

$ aignostics application [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • list: List available applications.
  • dump-schemata: Output the input schema of the application...
  • describe: Describe application.
  • run: List, submit and manage application runs

aignostics application list

List available applications.

Usage:

$ aignostics application list [OPTIONS]

Options:

  • --verbose / --no-verbose: Show application details [default: no-verbose]
  • --format TEXT: Output format: 'text' (default) or 'json' [default: text]
  • --help: Show this message and exit.

aignostics application dump-schemata

Output the input schema of the application in JSON format.

Usage:

$ aignostics application dump-schemata [OPTIONS] APPLICATION_ID

Arguments:

  • APPLICATION_ID: Id of the application or application_version to dump the output schema for. [required]

Options:

  • --application-version TEXT: Version of the application. If not provided, the latest version will be used.
  • --destination DIRECTORY: Path pointing to directory where the input and output schemata will be dumped. [default: (<current-working-directory>)]
  • --zip / --no-zip: If set, the schema files will be zipped into a single file, with the schema files deleted. [default: no-zip]
  • --help: Show this message and exit.

aignostics application describe

Describe application.

Usage:

$ aignostics application describe [OPTIONS] APPLICATION_ID

Arguments:

  • APPLICATION_ID: Id of the application to describe [required]

Options:

  • --verbose / --no-verbose: Show application details [default: no-verbose]
  • --format TEXT: Output format: 'text' (default) or 'json' [default: text]
  • --help: Show this message and exit.

aignostics application run

List, submit and manage application runs

Usage:

$ aignostics application run [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • execute: Prepare metadata, upload data to platform,...
  • prepare: Prepare metadata CSV file required for...
  • upload: Upload files referenced in the metadata...
  • submit: Submit run by referencing the metadata CSV...
  • list: List runs.
  • describe: Describe run.
  • dump-metadata: Dump custom metadata of a run as JSON to...
  • dump-item-metadata: Dump custom metadata of an item as JSON to...
  • cancel: Cancel run.
  • cancel-by-filter: Cancel runs matching filter criteria.
  • update-metadata: Update custom metadata for a run.
  • update-item-metadata: Update custom metadata for an item in a run.
  • result: Download or delete run results.

aignostics application run execute

Prepare metadata, upload data to platform, and submit an application run, then incrementally download results.

(1) Prepares metadata CSV file for the given application version by scanning the source directory for whole slide images and extracting metadata such as width, height, and mpp. (2) Optionally amends the metadata CSV file using the given mappings to set additional required attributes. (3) Uploads the files referenced in the metadata CSV file to the cloud bucket provisioned in the Aignostics platform. (4) Submits the run for the given application version with the metadata from the CSV file. (5) Downloads the results of the run to the destination directory, by default waiting for the run to complete and downloading results incrementally.

Usage:

$ aignostics application run execute [OPTIONS] APPLICATION_ID METADATA_CSV_FILE SOURCE_DIRECTORY

Arguments:

  • APPLICATION_ID: Id of application version to execute. [required]
  • METADATA_CSV_FILE: Filename of the .csv file containing the metadata and external ids. [required]
  • SOURCE_DIRECTORY: Source directory to scan for whole slide images [required]

Options:

  • --application-version TEXT: Version of the application. If not provided, the latest version will be used.
  • --mapping TEXT: Mapping to use for amending metadata CSV file. Each mapping is of the form '<regexp>:<key>=<value>,<key>=<value>,...'. The regular expression is matched against the external_id attribute of the entry. The key/value pairs are applied to the entry if the pattern matches. You can use the mapping option multiple times to set values for multiple files. Example: ".*:staining_method=H&E,tissue=LIVER,disease=LIVER_CANCER"
  • --create-subdirectory-for-run / --no-create-subdirectory-for-run: Create a subdirectory for the results of the run in the destination directory [default: create-subdirectory-for-run]
  • --create-subdirectory-per-item / --no-create-subdirectory-per-item: Create a subdirectory per item in the destination directory [default: create-subdirectory-per-item]
  • --upload-prefix TEXT: Prefix for the upload destination. If not given will be set to current milliseconds. [default: (<current-timestamp-ms>)]
  • --wait-for-completion / --no-wait-for-completion: Wait for run completion and download results incrementally [default: wait-for-completion]
  • --note TEXT: Optional note to include with the run submission via custom metadata.
  • --due-date TEXT: Optional soft due date to include with the run submission, ISO8601 format. The scheduler will try to complete the run by this date, taking the subscription tierand available GPU resources into account.
  • --deadline TEXT: Optional hard deadline to include with the run submission, ISO8601 format. If processing exceeds this deadline, the run can be aborted.
  • --onboard-to-aignostics-portal / --no-onboard-to-aignostics-portal: If True, onboard the run to the Aignostics Portal. [default: no-onboard-to-aignostics-portal]
  • --gpu-type TEXT: GPU type to use for processing (L4 or A100). [default: A100]
  • --gpu-provisioning-mode TEXT: GPU provisioning mode (SPOT, ON_DEMAND, or FLEX_START). [default: SPOT]
  • --max-gpus-per-slide INTEGER RANGE: Maximum number of GPUs to allocate per slide (1-8). [default: 1; 1<=x<=8]
  • --flex-start-max-run-duration-minutes INTEGER RANGE: Maximum run duration in minutes when using FLEX_START provisioning mode (1-3600). Ignored when gpu_provisioning_mode is not FLEX_START. [default: 720; 1<=x<=3600]
  • --cpu-provisioning-mode TEXT: CPU provisioning mode (SPOT or ON_DEMAND). [default: SPOT]
  • --node-acquisition-timeout-minutes INTEGER RANGE: Timeout for acquiring compute nodes in minutes (1-3600). [default: 30; 1<=x<=3600]
  • --force / --no-force: If True, skip the platform health check before proceeding. [default: no-force]
  • --help: Show this message and exit.

aignostics application run prepare

Prepare metadata CSV file required for submitting a run.

(1) Scans source_directory for whole slide images. (2) Extracts metadata from whole slide images such as width, height, mpp. (3) Creates CSV file with columns as required by the given application version. (4) Optionally applies mappings to amend the metadata CSV file for columns that are not automatically filled by the metadata extraction process.

Example: aignostics application run prepare "he-tme:v0.51.0" metadata.csv /path/to/source_directory --mapping ".*\.tiff:staining_method=H&E,tissue=LUNG,disease=LUNG_CANCER"

Usage:

$ aignostics application run prepare [OPTIONS] APPLICATION_ID METADATA_CSV SOURCE_DIRECTORY

Arguments:

  • APPLICATION_ID: Id of the application to generate the metadata for. [required]
  • METADATA_CSV: Target filename for the generated metadata CSV file. [required]
  • SOURCE_DIRECTORY: Source directory to scan for whole slide images [required]

Options:

  • --application-version TEXT: Version of the application. If not provided, the latest version will be used.
  • --mapping TEXT: Mapping to use for amending metadata CSV file. Each mapping is of the form '<regexp>:<key>=<value>,<key>=<value>,...'. The regular expression is matched against the external_id attribute of the entry. The key/value pairs are applied to the entry if the pattern matches. You can use the mapping option multiple times to set values for multiple files.
  • --help: Show this message and exit.

aignostics application run upload

Upload files referenced in the metadata CSV file to the Aignostics platform.

  1. Reads the metadata CSV file.
  2. Uploads the files referenced in the CSV file to the Aignostics platform.
  3. Incrementally updates the CSV file with upload progress and the signed URLs for the uploaded files.

Usage:

$ aignostics application run upload [OPTIONS] APPLICATION_ID METADATA_CSV_FILE

Arguments:

  • APPLICATION_ID: Id of the application to upload data for. [required]
  • METADATA_CSV_FILE: Filename of the .csv file containing the metadata and external ids. [required]

Options:

  • --application-version TEXT: Version of the application. If not provided, the latest version will be used.
  • --upload-prefix TEXT: Prefix for the upload destination. If not given will be set to current milliseconds. [default: (<current-timestamp-ms>)]
  • --onboard-to-aignostics-portal / --no-onboard-to-aignostics-portal: If set, the run will be onboarded to the Aignostics Portal. [default: no-onboard-to-aignostics-portal]
  • --force / --no-force: If True, skip the platform health check before proceeding. [default: no-force]
  • --help: Show this message and exit.

aignostics application run submit

Submit run by referencing the metadata CSV file.

  1. Requires the metadata CSV file to be generated and referenced files uploaded first

Returns: The ID of the submitted application run.

Usage:

$ aignostics application run submit [OPTIONS] APPLICATION_ID METADATA_CSV_FILE

Arguments:

  • APPLICATION_ID: Id of the application to submit run for. [required]
  • METADATA_CSV_FILE: Filename of the .csv file containing the metadata and external ids. [required]

Options:

  • --application-version TEXT: Version of the application. If not provided, the latest version will be used.
  • --note TEXT: Optional note to include with the run submission via custom metadata.
  • --tags TEXT: Optional comma-separated list of tags to attach to the run for filtering.
  • --due-date TEXT: Optional soft due date to include with the run submission, ISO8601 format. The scheduler will try to complete the run by this date, taking the subscription tierand available GPU resources into account.
  • --deadline TEXT: Optional hard deadline to include with the run submission, ISO8601 format. If processing exceeds this deadline, the run can be aborted.
  • --onboard-to-aignostics-portal / --no-onboard-to-aignostics-portal: If True, onboard the run to the Aignostics Portal. [default: no-onboard-to-aignostics-portal]
  • --gpu-type TEXT: GPU type to use for processing (L4 or A100). [default: A100]
  • --gpu-provisioning-mode TEXT: GPU provisioning mode (SPOT, ON_DEMAND, or FLEX_START). [default: SPOT]
  • --max-gpus-per-slide INTEGER RANGE: Maximum number of GPUs to allocate per slide (1-8). [default: 1; 1<=x<=8]
  • --flex-start-max-run-duration-minutes INTEGER RANGE: Maximum run duration in minutes when using FLEX_START provisioning mode (1-3600). Ignored when gpu_provisioning_mode is not FLEX_START. [default: 720; 1<=x<=3600]
  • --cpu-provisioning-mode TEXT: CPU provisioning mode (SPOT or ON_DEMAND). [default: SPOT]
  • --node-acquisition-timeout-minutes INTEGER RANGE: Timeout for acquiring compute nodes in minutes (1-3600). [default: 30; 1<=x<=3600]
  • --force / --no-force: If True, skip the platform health check before proceeding. [default: no-force]
  • --help: Show this message and exit.

aignostics application run list

List runs.

Usage:

$ aignostics application run list [OPTIONS]

Options:

  • --verbose / --no-verbose: Show application details [default: no-verbose]
  • --limit INTEGER: Maximum number of runs to display
  • --tags TEXT: Optional comma-separated list of tags to filter runs. All tags must match.
  • --note-regex TEXT: Optional regex pattern to filter runs by note metadata.
  • --query TEXT: Optional query string to filter runs by note OR tags.
  • --note-case-insensitive / --no-note-case-insensitive: Make note regex search case-insensitive. [default: note-case-insensitive]
  • --format TEXT: Output format: 'text' (default) or 'json' [default: text]
  • --help: Show this message and exit.

aignostics application run describe

Describe run.

Usage:

$ aignostics application run describe [OPTIONS] RUN_ID

Arguments:

  • RUN_ID: Id of the run to describe [required]

Options:

  • --format TEXT: Output format: 'text' (default) or 'json' [default: text]
  • -s, --summarize: Show only run and item status summary (external ID, state, error message)
  • --help: Show this message and exit.

aignostics application run dump-metadata

Dump custom metadata of a run as JSON to stdout.

Usage:

$ aignostics application run dump-metadata [OPTIONS] RUN_ID

Arguments:

  • RUN_ID: Id of the run to dump custom metadata for [required]

Options:

  • --pretty / --no-pretty: Pretty print JSON output with indentation [default: no-pretty]
  • --help: Show this message and exit.

aignostics application run dump-item-metadata

Dump custom metadata of an item as JSON to stdout.

Usage:

$ aignostics application run dump-item-metadata [OPTIONS] RUN_ID EXTERNAL_ID

Arguments:

  • RUN_ID: Id of the run containing the item [required]
  • EXTERNAL_ID: External ID of the item to dump custom metadata for [required]

Options:

  • --pretty / --no-pretty: Pretty print JSON output with indentation [default: no-pretty]
  • --help: Show this message and exit.

aignostics application run cancel

Cancel run.

Usage:

$ aignostics application run cancel [OPTIONS] RUN_ID

Arguments:

  • RUN_ID: Id of the run to cancel [required]

Options:

  • --help: Show this message and exit.

aignostics application run cancel-by-filter

Cancel runs matching filter criteria.

All provided filters must match for a run to be canceled. At least one filter parameter (tags, application_id, or application_version) must be provided.

Usage:

$ aignostics application run cancel-by-filter [OPTIONS]

Options:

  • --tags TEXT: Optional comma-separated list of tags to filter runs. All tags must match.
  • --application-id TEXT: Optional application ID to filter runs.
  • --application-version TEXT: Optional application version to filter runs.
  • --limit INTEGER: Maximum number of runs to cancel
  • --dry-run / --no-dry-run: Show which runs would be canceled without actually canceling them. [default: no-dry-run]
  • --help: Show this message and exit.

aignostics application run update-metadata

Update custom metadata for a run.

Usage:

$ aignostics application run update-metadata [OPTIONS] RUN_ID METADATA_JSON

Arguments:

  • RUN_ID: Id of the run to update [required]
  • METADATA_JSON: Custom metadata as JSON string (e.g., '{"key": "value"}') [required]

Options:

  • --help: Show this message and exit.

aignostics application run update-item-metadata

Update custom metadata for an item in a run.

Usage:

$ aignostics application run update-item-metadata [OPTIONS] RUN_ID EXTERNAL_ID METADATA_JSON

Arguments:

  • RUN_ID: Id of the run containing the item [required]
  • EXTERNAL_ID: External ID of the item to update [required]
  • METADATA_JSON: Custom metadata as JSON string (e.g., '{"key": "value"}') [required]

Options:

  • --help: Show this message and exit.

aignostics application run result

Download or delete run results.

Usage:

$ aignostics application run result [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • download: Download results of a run.
  • delete: Delete results of run.
aignostics application run result download

Download results of a run.

Usage:

$ aignostics application run result download [OPTIONS] RUN_ID [DESTINATION_DIRECTORY]

Arguments:

  • RUN_ID: Id of the run to download results for [required]
  • [DESTINATION_DIRECTORY]: Destination directory to download results to [default: (~/Library/Application Support/aignostics/results)]

Options:

  • --create-subdirectory-for-run / --no-create-subdirectory-for-run: Create a subdirectory for the results of the run in the destination directory [default: create-subdirectory-for-run]
  • --create-subdirectory-per-item / --no-create-subdirectory-per-item: Create a subdirectory per item in the destination directory [default: create-subdirectory-per-item]
  • --wait-for-completion / --no-wait-for-completion: Wait for run completion and download results incrementally [default: wait-for-completion]
  • --qupath-project / --no-qupath-project: Create a QuPath project referencing input slides and results. The QuPath project will be created in a subfolder of the destination directory. This option requires the QuPath extension for Launchpad: start the Launchpad with uvx --with &quot;aignostics&quot; aignostics ... This options requires installation of the QuPath application: Run uvx --with "aignostics" aignostics qupath install [default: no-qupath-project]
  • --help: Show this message and exit.
aignostics application run result delete

Delete results of run.

Usage:

$ aignostics application run result delete [OPTIONS] RUN_ID

Arguments:

  • RUN_ID: Id of the run to delete results for [required]

Options:

  • --help: Show this message and exit.

aignostics bucket

Operations on cloud bucket on Aignostics Platform.

Usage:

$ aignostics bucket [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • upload: Upload file or directory to bucket in...
  • find: Find objects in bucket on Aignostics...
  • download: Download objects from bucket in Aignostics...
  • delete: Delete objects in bucket on Aignostics...
  • purge: Purge all objects in bucket on Aignostics...

aignostics bucket upload

Upload file or directory to bucket in Aignostics platform.

Usage:

$ aignostics bucket upload [OPTIONS] SOURCE

Arguments:

  • SOURCE: Source file or directory to upload [required]

Options:

  • --destination-prefix TEXT: Destination layout. Supports {username}, {timestamp}. E.g. you might want to use "{username}/myproject/" [default: {username}]
  • --help: Show this message and exit.

aignostics bucket find

Find objects in bucket on Aignostics Platform.

Usage:

$ aignostics bucket find [OPTIONS] [WHAT]...

Arguments:

  • [WHAT]...: Patterns or keys to match object keys against - all if not specified.

Options:

  • --what-is-key / --no-what-is-key: Specify if 'what' is a single object key. If not specified, 'what' is treated as a regex pattern. [default: no-what-is-key]
  • --detail / --no-detail: Show details [default: no-detail]
  • --signed-urls: Include signed download URLs
  • --help: Show this message and exit.

aignostics bucket download

Download objects from bucket in Aignostics platform to local directory.

Usage:

$ aignostics bucket download [OPTIONS] [WHAT]...

Arguments:

  • [WHAT]...: Patterns or keys to match object keys against - all if not specified.

Options:

  • --what-is-key / --no-what-is-key: Specify if 'what' is a single object key. If not specified, 'what' is treated as a regex pattern. [default: no-what-is-key]
  • --destination DIRECTORY: Destination directory to download the matching objects to. [default: (~/Library/Application Support/aignostics/bucket_downloads)]
  • --help: Show this message and exit.

aignostics bucket delete

Delete objects in bucket on Aignostics Platform.

Usage:

$ aignostics bucket delete [OPTIONS] WHAT...

Arguments:

  • WHAT...: Patterns or keys to match object keys against. [required]

Options:

  • --what-is-key / --no-what-is-key: Specify if 'what' is a single object key. If not specified, 'what' is treated as a regex pattern. [default: no-what-is-key]
  • --dry-run / --no-dry-run: If set, only determines number of items that would be deleted, without actually deleting. [default: dry-run]
  • --help: Show this message and exit.

aignostics bucket purge

Purge all objects in bucket on Aignostics Platform.

Usage:

$ aignostics bucket purge [OPTIONS]

Options:

  • --dry-run / --no-dry-run: If set, only determines number of items that would be deleted, without actually deleting. [default: dry-run]
  • --help: Show this message and exit.

aignostics dataset

Download datasets from National Institute of Cancer (NIC) and Aignostics.

Usage:

$ aignostics dataset [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • idc: Download public datasets from Image Data...
  • aignostics: Download proprietary sample datasets from...

aignostics dataset idc

Download public datasets from Image Data Commons (IDC) Portal of National Institute of Cancer (NIC).

Usage:

$ aignostics dataset idc [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • browse: Open browser to explore IDC portal.
  • indices: List available columns in given of the IDC...
  • columns: List available columns in given of the IDC...
  • query: Query IDC index.
  • download: Download from manifest file, identifier,...

aignostics dataset idc browse

Open browser to explore IDC portal.

Usage:

$ aignostics dataset idc browse [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics dataset idc indices

List available columns in given of the IDC Portal.

Usage:

$ aignostics dataset idc indices [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics dataset idc columns

List available columns in given of the IDC Portal.

Usage:

$ aignostics dataset idc columns [OPTIONS]

Options:

  • --index TEXT: List available columns in given of the IDC Portal. See List available columns in given of the IDC Portal for available indices [default: sm_instance_index]
  • --help: Show this message and exit.

aignostics dataset idc query

Query IDC index. For example queries see https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/labs/idc_rsna2023.ipynb.

Usage:

$ aignostics dataset idc query [OPTIONS] [QUERY]

Arguments:

  • [QUERY]: SQL Query to execute.See https://idc-index.readthedocs.io/en/latest/column_descriptions.html for indices and their attributes [default: SELECT SOPInstanceUID, SeriesInstanceUID, ImageType[3], instance_size, TotalPixelMatrixColumns, TotalPixelMatrixRows FROM sm_instance_index WHERE TotalPixelMatrixColumns > 25000 AND TotalPixelMatrixRows > 25000 AND ImageType[3] = 'VOLUME' ]

Options:

  • --indices TEXT: Comma separated list of additional indices to sync before running the query. The main index is always present. By default sm_instance_index is synched in addition. See https://idc-index.readthedocs.io/en/latest/column_descriptions.html for available indices. [default: sm_instance_index]
  • --help: Show this message and exit.

aignostics dataset idc download

Download from manifest file, identifier, or comma-separate set of identifiers.

Usage:

$ aignostics dataset idc download [OPTIONS] SOURCE [TARGET]

Arguments:

  • SOURCE: Identifier or comma-separated set of identifiers. IDs matched against collection_id, PatientId, StudyInstanceUID, SeriesInstanceUID or SOPInstanceUID. Example: 1.3.6.1.4.1.5962.99.1.1069745200.1645485340.1637452317744.2.0 [required]
  • [TARGET]: target directory for download [default: (~/Library/Application Support/aignostics/datasets/idc)]

Options:

  • --target-layout TEXT: layout of the target directory. See default for available elements for use [default: %collection_id/%PatientID/%StudyInstanceUID/%Modality_%SeriesInstanceUID/]
  • --dry-run / --no-dry-run: dry run [default: no-dry-run]
  • --help: Show this message and exit.

aignostics dataset aignostics

Download proprietary sample datasets from Aignostics.

Usage:

$ aignostics dataset aignostics [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • download: Download from bucket to folder via a...

aignostics dataset aignostics download

Download from bucket to folder via a bucket URL.

Usage:

$ aignostics dataset aignostics download [OPTIONS] SOURCE_URL [DESTINATION_DIRECTORY]

Arguments:

  • SOURCE_URL: URL to download. Example: gs://aignx-storage-service-dev/sample_data_formatted/9375e3ed-28d2-4cf3-9fb9-8df9d11a6627.tiff [required]
  • [DESTINATION_DIRECTORY]: Destination directory to download to [default: (~/Library/Application Support/aignostics/datasets/aignostics)]

Options:

  • --help: Show this message and exit.

aignostics sdk

Platform operations such as dumping the SDK metadata schema.

Usage:

$ aignostics sdk [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • run-metadata-schema: Print the JSON Schema for Run SDK metadata.
  • item-metadata-schema: Print the JSON Schema for Item SDK metadata.

aignostics sdk run-metadata-schema

Print the JSON Schema for Run SDK metadata.

This schema defines the structure and validation rules for metadata that the SDK attaches to application runs. Use this to understand what fields are expected and their types.

Usage:

$ aignostics sdk run-metadata-schema [OPTIONS]

Options:

  • --pretty / --no-pretty: Pretty print JSON output [default: pretty]
  • --help: Show this message and exit.

aignostics sdk item-metadata-schema

Print the JSON Schema for Item SDK metadata.

This schema defines the structure and validation rules for metadata that the SDK attaches to individual items within application runs. Use this to understand what fields are expected and their types.

Usage:

$ aignostics sdk item-metadata-schema [OPTIONS]

Options:

  • --pretty / --no-pretty: Pretty print JSON output [default: pretty]
  • --help: Show this message and exit.

aignostics user

User operations such as login, logout and whoami.

Usage:

$ aignostics user [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • logout: Logout if authenticated.
  • login: (Re)login.
  • whoami: Print user info.

aignostics user logout

Logout if authenticated.

  • Deletes the cached authentication token if existing.

Usage:

$ aignostics user logout [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics user login

(Re)login.

Usage:

$ aignostics user login [OPTIONS]

Options:

  • --relogin / --no-relogin: Re-login [default: no-relogin]
  • --help: Show this message and exit.

aignostics user whoami

Print user info.

Usage:

$ aignostics user whoami [OPTIONS]

Options:

  • --mask-secrets / --no-mask-secrets: Mask secrets [default: mask-secrets]
  • --relogin / --no-relogin: Re-login [default: no-relogin]
  • --help: Show this message and exit.

aignostics qupath

Interact with QuPath application.

Usage:

$ aignostics qupath [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • install: Install QuPath application.
  • launch: Launch QuPath application.
  • processes: List running QuPath processes.
  • terminate: Terminate running QuPath processes.
  • uninstall: Uninstall QuPath application.
  • add: Add image(s) to QuPath project.
  • annotate: Add image(s) to QuPath project.
  • inspect: Inspect project.
  • run-script: Run a QuPath Groovy script with optional...

aignostics qupath install

Install QuPath application.

Usage:

$ aignostics qupath install [OPTIONS]

Options:

  • --version TEXT: Version of QuPath to install. Do not change this unless you know what you are doing. [default: 0.6.0]
  • --path DIRECTORY: Path to install QuPath to. If not specified, the default installation path will be used.Do not change this unless you know what you are doing. [default: (~/Library/Application Support/aignostics)]
  • --reinstall / --no-reinstall: Reinstall QuPath even if it is already installed. This will overwrite the existing installation. [default: reinstall]
  • --platform-system TEXT: Override the system to assume for the installation. This is useful for testing purposes. [default: Darwin]
  • --platform-machine TEXT: Override the machine architecture to assume for the installation. This is useful for testing purposes. [default: arm64]
  • --help: Show this message and exit.

aignostics qupath launch

Launch QuPath application.

Usage:

$ aignostics qupath launch [OPTIONS]

Options:

  • --project DIRECTORY: Path to QuPath project directory.
  • --image TEXT: Path to image. Must be part of QuPath project
  • --script FILE: Path to QuPath script to run on launch. Must be part of QuPath project.
  • --help: Show this message and exit.

aignostics qupath processes

List running QuPath processes.

Notice: This will not list processes that are not started from the installation directory.

Usage:

$ aignostics qupath processes [OPTIONS]

Options:

  • -j, --json: Output the running QuPath processes as JSON.
  • --help: Show this message and exit.

aignostics qupath terminate

Terminate running QuPath processes.

Notice: This will not terminate processes that are not started from the installation directory.

Usage:

$ aignostics qupath terminate [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics qupath uninstall

Uninstall QuPath application.

Usage:

$ aignostics qupath uninstall [OPTIONS]

Options:

  • --version TEXT: Version of QuPath to install. If not specified, all versions will be uninstalled.
  • --path DIRECTORY: Path to install QuPath to. If not specified, the default installation path will be used.Do not change this unless you know what you are doing. [default: (~/Library/Application Support/aignostics)]
  • --platform-system TEXT: Override the system to assume for the installation. This is useful for testing purposes. [default: Darwin]
  • --platform-machine TEXT: Override the machine architecture to assume for the installation. This is useful for testing purposes. [default: arm64]
  • --help: Show this message and exit.

aignostics qupath add

Add image(s) to QuPath project. Creates project if it does not exist.

Usage:

$ aignostics qupath add [OPTIONS] PROJECT PATH...

Arguments:

  • PROJECT: Path to QuPath project directory. Will be created if it does not exist. [required]
  • PATH...: One or multiple paths. A path can point to an individual image or folder.In case of a folder, all images within will be added for supported image types. [required]

Options:

  • --help: Show this message and exit.

aignostics qupath annotate

Add image(s) to QuPath project. Creates project if it does not exist.

Usage:

$ aignostics qupath annotate [OPTIONS] PROJECT IMAGE ANNOTATIONS

Arguments:

  • PROJECT: Path to QuPath project directory. Will be created if it does not exist. [required]
  • IMAGE: Path to image to annotate. If the image is not part of the project, it will be added. [required]
  • ANNOTATIONS: Path to polygons file to import. The file must be a compatible GeoJSON file. [required]

Options:

  • --help: Show this message and exit.

aignostics qupath inspect

Inspect project.

Usage:

$ aignostics qupath inspect [OPTIONS] PROJECT

Arguments:

  • PROJECT: Path to QuPath project directory. [required]

Options:

  • --help: Show this message and exit.

aignostics qupath run-script

Run a QuPath Groovy script with optional arguments.

Usage:

$ aignostics qupath run-script [OPTIONS] SCRIPT

Arguments:

  • SCRIPT: Path to the Groovy script file to execute. [required]

Options:

  • -p, --project DIRECTORY: Path to the QuPath project directory.
  • -i, --image TEXT: Name of the image in the project or path to image file.
  • -a, --args TEXT: Arguments to pass to the script. Can be specified multiple times.
  • --help: Show this message and exit.

aignostics system

Determine health, info and further utillities.

Usage:

$ aignostics system [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • health: Determine and print system health.
  • info: Determine and print system info.
  • dump-dot-env-file: Dump settings to .env file.
  • serve: Start the web server, hosting the...
  • openapi: Dump the OpenAPI specification.
  • install: Complete installation.
  • config: Configure application settings.

aignostics system health

Determine and print system health.

Args: output_format (OutputFormat): Output format (JSON or YAML).

Usage:

$ aignostics system health [OPTIONS]

Options:

  • --output-format [yaml|json]: Output format [default: json]
  • --help: Show this message and exit.

aignostics system info

Determine and print system info.

Args: include_environ (bool): Include environment variables. mask_secrets (bool): Mask values for variables identified as secrets. output_format (OutputFormat): Output format (JSON or YAML).

Usage:

$ aignostics system info [OPTIONS]

Options:

  • --include-environ / --no-include-environ: Include environment variables [default: no-include-environ]
  • --mask-secrets / --no-mask-secrets: Mask secrets [default: mask-secrets]
  • --output-format [yaml|json]: Output format [default: json]
  • --help: Show this message and exit.

aignostics system dump-dot-env-file

Dump settings to .env file.

Args: destination (Path): Path pointing to .env file to generate.

Usage:

$ aignostics system dump-dot-env-file [OPTIONS]

Options:

  • --destination FILE: Path pointing to .env file to gnerate, defaults to .env.current in current working directory. [default: .env.current]
  • --help: Show this message and exit.

aignostics system serve

Start the web server, hosting the graphical web application and/or webservice API.

Args: host (str): Host to bind the server to. port (int): Port to bind the server to. open_browser (bool): Open app in browser after starting the server.

Usage:

$ aignostics system serve [OPTIONS]

Options:

  • --host TEXT: Host to bind the server to [default: 127.0.0.1]
  • --port INTEGER: Port to bind the server to [default: 8000]
  • --open-browser / --no-open-browser: Open app in browser after starting the server [default: no-open-browser]
  • --help: Show this message and exit.

aignostics system openapi

Dump the OpenAPI specification.

Args: api_version (str): API version to dump. output_format (OutputFormat): Output format (JSON or YAML).

Raises: typer.Exit: If an invalid API version is provided.

Usage:

$ aignostics system openapi [OPTIONS]

Options:

  • --api-version TEXT: API Version. Available: v1 [default: v1]
  • --output-format [yaml|json]: Output format [default: json]
  • --help: Show this message and exit.

aignostics system install

Complete installation.

Usage:

$ aignostics system install [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics system config

Configure application settings.

Usage:

$ aignostics system config [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • get: Set a configuration key to a value.
  • set: Set a configuration key to a value.
  • unset: Set a configuration key to a value.
  • remote-diagnostics-enable: Enable remote diagnostics via Sentry and...
  • remote-diagnostics-disable: Disable remote diagnostics.
  • http-proxy-enable: Enable HTTP proxy.
  • http-proxy-disable: Disable HTTP proxy.

aignostics system config get

Set a configuration key to a value.

Usage:

$ aignostics system config get [OPTIONS] KEY

Arguments:

  • KEY: Configuration key to get value for [required]

Options:

  • --help: Show this message and exit.

aignostics system config set

Set a configuration key to a value.

Usage:

$ aignostics system config set [OPTIONS] KEY VALUE

Arguments:

  • KEY: Configuration key to set [required]
  • VALUE: Value to set for the configuration key [required]

Options:

  • --help: Show this message and exit.

aignostics system config unset

Set a configuration key to a value.

Usage:

$ aignostics system config unset [OPTIONS] KEY

Arguments:

  • KEY: Configuration key to unset [required]

Options:

  • --help: Show this message and exit.

aignostics system config remote-diagnostics-enable

Enable remote diagnostics via Sentry and Logfire. Data stored in EU data centers.

Usage:

$ aignostics system config remote-diagnostics-enable [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics system config remote-diagnostics-disable

Disable remote diagnostics.

Usage:

$ aignostics system config remote-diagnostics-disable [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics system config http-proxy-enable

Enable HTTP proxy.

Usage:

$ aignostics system config http-proxy-enable [OPTIONS]

Options:

  • --host TEXT: Host [default: proxy.charite.de]
  • --port INTEGER: Port [default: 8080]
  • --scheme TEXT: Scheme [default: http]
  • --ssl-cert-file TEXT: SSL certificate file
  • --no-ssl-verify / --no-no-ssl-verify: Disable SSL verification [default: no-no-ssl-verify]
  • --help: Show this message and exit.

aignostics system config http-proxy-disable

Disable HTTP proxy.

Usage:

$ aignostics system config http-proxy-disable [OPTIONS]

Options:

  • --help: Show this message and exit.

aignostics wsi

Operations on whole slide images.

Usage:

$ aignostics wsi [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • inspect: Inspect a wsi file and display its metadata.
  • dicom: Workaround for Typer bug, see...

aignostics wsi inspect

Inspect a wsi file and display its metadata.

Usage:

$ aignostics wsi inspect [OPTIONS] PATH

Arguments:

  • PATH: Path to the wsi file [required]

Options:

  • --help: Show this message and exit.

aignostics wsi dicom

Workaround for Typer bug, see fastapi/typer#1240.

Raises: typer.Exit: If no subcommand is invoked, prints the help message and exits.

Usage:

$ aignostics wsi dicom [OPTIONS] COMMAND [ARGS]...

Options:

  • --help: Show this message and exit.

Commands:

  • inspect: Inspect DICOM files at any hierarchy level.
  • geojson_import: Import GeoJSON annotations into DICOM ANN...

aignostics wsi dicom inspect

Inspect DICOM files at any hierarchy level.

Usage:

$ aignostics wsi dicom inspect [OPTIONS] PATH

Arguments:

  • PATH: Path of file or directory to inspect [required]

Options:

  • --verbose / --no-verbose: Verbose output [default: no-verbose]
  • --summary / --no-summary: Show only summary information [default: no-summary]
  • --wsi-only / --no-wsi-only: Filter to WSI files only [default: no-wsi-only]
  • --help: Show this message and exit.

aignostics wsi dicom geojson_import

Import GeoJSON annotations into DICOM ANN instance.

Usage:

$ aignostics wsi dicom geojson_import [OPTIONS] DICOM_PATH GEOJSON_PATH

Arguments:

  • DICOM_PATH: Path to the DICOM file [required]
  • GEOJSON_PATH: Path to the GeoJSON file [required]

Options:

  • --help: Show this message and exit.