Bioimage Archive Tools#

Configuration File: bioimage_archive_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

BioImageArchive_get_study (Type: BioImageArchiveTool)#

Get detailed information about a specific BioImage Archive study by accession number. Returns com…

BioImageArchive_get_study tool specification

Tool Information:

  • Name: BioImageArchive_get_study

  • Type: BioImageArchiveTool

  • Description: Get detailed information about a specific BioImage Archive study by accession number. Returns comprehensive metadata including title, description, imaging methods, organism, and file information. Example: ‘S-BIAD634’ returns an annotated fluorescence image dataset.

Parameters:

  • accession (string) (required) BioImage Archive study accession number. Format: S-BIAD#### or S-BSST#### or S-EPMC#######. Examples: ‘S-BIAD634’, ‘S-BIAD928’.

Example Usage:

query = {
    "name": "BioImageArchive_get_study",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

BioImageArchive_list_study_files (Type: BioImageArchiveTool)#

List the file/image manifest of a BioImage Archive study, giving per-file download paths and per-…

BioImageArchive_list_study_files tool specification

Tool Information:

  • Name: BioImageArchive_list_study_files

  • Type: BioImageArchiveTool

  • Description: List the file/image manifest of a BioImage Archive study, giving per-file download paths and per-image experimental annotations. Unlike BioImageArchive_get_study (which returns study-level metadata), this returns the actual files: image Name, relative download path, size, and submitter annotations. Use limit/offset to page through large manifests; metadata preserves records_total and records_filtered and provides has_more and next_offset so every file is reachable.

Parameters:

  • accession (string) (required) BioImage Archive study accession. Format S-BIAD#### / S-BSST#### (e.g. ‘S-BIAD144’). Obtain from BioImageArchive_search_studies.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of files to return (default 25, max 500). Values outside this range return an error rather than being silently changed.

  • offset ([‘integer’, ‘null’]) (optional) Number of files to skip for pagination (default 0). Continue with metadata.next_offset while metadata.has_more is true.

Example Usage:

query = {
    "name": "BioImageArchive_list_study_files",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

BioImageArchive_search_bioimages (Type: BioImageArchiveTool)#

Search the BioImages collection with explicit page pagination. Metadata reports next_page and pre…

BioImageArchive_search_bioimages tool specification

Tool Information:

  • Name: BioImageArchive_search_bioimages

  • Type: BioImageArchiveTool

  • Description: Search the BioImages collection with explicit page pagination. Metadata reports next_page and preserves the upstream isTotalHitsExact qualifier. When total_hits_relation is lower_bound, total_hits is only a lower bound rather than the true total; continue until pagination ends.

Parameters:

  • query (string) (required) Search query for biological imaging data. Examples: ‘cell division’, ‘neuron morphology’, ‘tissue section’, ‘live cell imaging’.

  • page_size ([‘integer’, ‘null’]) (optional) Number of results per page. Default: 10. Max: 100.

  • page (integer) (optional) One-based result page. Continue with metadata.next_page.

Example Usage:

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

BioImageArchive_search_studies (Type: BioImageArchiveTool)#

Search the BioImage Archive (EBI BioStudies) for biological imaging datasets with explicit page n…

BioImageArchive_search_studies tool specification

Tool Information:

  • Name: BioImageArchive_search_studies

  • Type: BioImageArchiveTool

  • Description: Search the BioImage Archive (EBI BioStudies) for biological imaging datasets with explicit page navigation. The BioImage Archive hosts open microscopy, imaging, and visualization data from life sciences research. Search by imaging modality, organism, technique, or topic. Metadata preserves BioStudies’ isTotalHitsExact qualifier: when total_hits_relation is lower_bound, total_hits must not be reported as the exact number of matches; continue through next_page until pagination ends.

Parameters:

  • query (string) (required) Search query - imaging modality, organism, technique, or topic. Examples: ‘cryo-EM’, ‘fluorescence microscopy’, ‘cell segmentation’, ‘brain imaging’, ‘protein localization’.

  • page_size ([‘integer’, ‘null’]) (optional) Number of results per page. Default: 10. Max: 100.

  • page ([‘integer’, ‘null’]) (optional) Page number (1-indexed). Default: 1. Continue with metadata.next_page.

Example Usage:

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