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 (append to the study’s FTP/HTTPS root), file size, and any annotation columns the submitters attached to each image (e.g. staining, cells, treatment, channels, timepoint). Use limit/offset to page through large manifests; metadata.records_total gives the full file count. Example: S-BIAD144 has 223 files; the first is ‘experimentA_01_WT_PDMP.czi’ (path experiments/experimentA_01_WT_PDMP.czi) with annotations staining=’click chemistry and IF’, cells=’WT’, treatment=’20 uM PDMP’, Channel_1=’pacSph’, Channel_2=’Lamp1’.

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).

  • offset ([‘integer’, ‘null’]) (optional) Number of files to skip for pagination (default 0).

Example Usage:

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

BioImageArchive_search_bioimages (Type: BioImageArchiveTool)

Search the BioImage Archive specifically for biological image datasets (BioImages collection). Th…

BioImageArchive_search_bioimages tool specification

Tool Information:

  • Name: BioImageArchive_search_bioimages

  • Type: BioImageArchiveTool

  • Description: Search the BioImage Archive specifically for biological image datasets (BioImages collection). This targets the BioImages-specific collection at EBI, returning imaging studies with microscopy-specific metadata. Example: ‘cell division’ finds imaging datasets of cell division processes.

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.

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. The BioImage Archiv…

BioImageArchive_search_studies tool specification

Tool Information:

  • Name: BioImageArchive_search_studies

  • Type: BioImageArchiveTool

  • Description: Search the BioImage Archive (EBI BioStudies) for biological imaging datasets. The BioImage Archive hosts open microscopy, imaging, and visualization data from life sciences research. Search by imaging modality (cryo-EM, fluorescence, confocal), organism, technique, or scientific topic. Returns study accessions, titles, and metadata. Example: ‘fluorescence microscopy cell’ finds fluorescence imaging studies.

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.

Example Usage:

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