Idr Tools

Configuration File: idr_tools.json Tool Type: Local Tools Count: 5

This page contains all tools defined in the idr_tools.json configuration file.

Available Tools

IDR_get_image_map_annotations (Type: BaseRESTTool)

Fetch the map (key-value) annotations attached to a specific IDR image. Map annotations carry the…

IDR_get_image_map_annotations tool specification

Tool Information:

  • Name: IDR_get_image_map_annotations

  • Type: BaseRESTTool

  • Description: Fetch the map (key-value) annotations attached to a specific IDR image. Map annotations carry the experimental metadata that scientists query IDR for: Gene Symbol, Gene Identifier (Ensembl), Cell Line, Antibody / Antibody Target, Phenotype, organism, and assay-specific keys. Returns a list of annotations, each with a ‘values’ array of [key, value] pairs. Obtain image IDs first from IDR_list_dataset_images. Example: image 1884807 returns 6 map annotations including Cell Line=HeLa, Gene Symbol=CDK5RAP2, Gene Identifier=ENSG00000136861, Antibody Target=CDK5RAP2-C.

Parameters:

  • image (integer) (required) IDR image ID (e.g. 1884807). Obtain from IDR_list_dataset_images.

Example Usage:

query = {
    "name": "IDR_get_image_map_annotations",
    "arguments": {
        "image": 10
    }
}
result = tu.run(query)

IDR_get_study (Type: BaseRESTTool)

Get detailed information about a specific imaging study (project) in the Image Data Resource (IDR…

IDR_get_study tool specification

Tool Information:

  • Name: IDR_get_study

  • Type: BaseRESTTool

  • Description: Get detailed information about a specific imaging study (project) in the Image Data Resource (IDR) by its project ID. Returns study metadata including name, description, number of datasets, and links to associated imaging data. Use IDR_list_studies to find study IDs.

Parameters:

  • project_id (integer) (required) IDR project/study ID (e.g., 101 for idr0018-neff-histopathology). Obtain from IDR_list_studies.

Example Usage:

query = {
    "name": "IDR_get_study",
    "arguments": {
        "project_id": 10
    }
}
result = tu.run(query)

IDR_get_study_datasets (Type: BaseRESTTool)

Get datasets (image collections) within a specific IDR imaging study. Each dataset within an IDR …

IDR_get_study_datasets tool specification

Tool Information:

  • Name: IDR_get_study_datasets

  • Type: BaseRESTTool

  • Description: Get datasets (image collections) within a specific IDR imaging study. Each dataset within an IDR project corresponds to a set of related images, often representing a specific experimental condition, cell line, or time point. Returns dataset names and IDs. Use IDR_list_studies to find study IDs first.

Parameters:

  • project_id (integer) (required) IDR project/study ID (e.g., 101). Obtain from IDR_list_studies.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of datasets to return (default 25, max 1000)

  • offset ([‘integer’, ‘null’]) (optional) Offset for pagination

Example Usage:

query = {
    "name": "IDR_get_study_datasets",
    "arguments": {
        "project_id": 10
    }
}
result = tu.run(query)

IDR_list_dataset_images (Type: BaseRESTTool)

List the individual images contained in a specific IDR (Image Data Resource) dataset, drilling do…

IDR_list_dataset_images tool specification

Tool Information:

  • Name: IDR_list_dataset_images

  • Type: BaseRESTTool

  • Description: List the individual images contained in a specific IDR (Image Data Resource) dataset, drilling down from the dataset level to the per-image level. Each IDR dataset (a collection of related microscopy images, e.g. one experimental plate or condition) contains many images; this tool returns their image IDs and names. Use the returned image IDs to fetch per-image map annotations (IDR_get_image_map_annotations), thumbnails, or pixel data. Obtain dataset IDs first from IDR_get_study_datasets. Supports limit/offset pagination; meta.totalCount gives the total number of images in the dataset.

Parameters:

  • dataset_id (integer) (required) IDR dataset ID (e.g. 51). Obtain from IDR_get_study_datasets.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of images to return (default 25, max 1000).

  • offset ([‘integer’, ‘null’]) (optional) Offset for pagination.

Example Usage:

query = {
    "name": "IDR_list_dataset_images",
    "arguments": {
        "dataset_id": 10
    }
}
result = tu.run(query)

IDR_list_studies (Type: BaseRESTTool)

List imaging studies (projects) from the Image Data Resource (IDR), the public repository for ref…

IDR_list_studies tool specification

Tool Information:

  • Name: IDR_list_studies

  • Type: BaseRESTTool

  • Description: List imaging studies (projects) from the Image Data Resource (IDR), the public repository for reference image datasets from published scientific studies. IDR contains high-content microscopy, histopathology, and other biological imaging datasets from over 140 studies. Returns study names (e.g., ‘idr0018-neff-histopathology/experimentA’), descriptions, IDs, and URLs to access datasets within each study.

Parameters:

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of studies to return (default 25, max 1000)

  • offset ([‘integer’, ‘null’]) (optional) Offset for pagination

Example Usage:

query = {
    "name": "IDR_list_studies",
    "arguments": {
    }
}
result = tu.run(query)