Allen Brain Tools

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

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

Available Tools

AllenBrain_get_expression_datasets (Type: AllenBrainTool)

Get gene expression experiment datasets from the Allen Mouse Brain Atlas for a given gene. Return…

AllenBrain_get_expression_datasets tool specification

Tool Information:

  • Name: AllenBrain_get_expression_datasets

  • Type: AllenBrainTool

  • Description: Get gene expression experiment datasets from the Allen Mouse Brain Atlas for a given gene. Returns section data sets including plane of section, section thickness, and linked gene info. These datasets contain ISH (in situ hybridization) gene expression images. Example: ‘Gad1’ returns 22 ISH experiment datasets.

Parameters:

  • gene_acronym (string) (required) Gene symbol/acronym. Examples: ‘Gad1’, ‘Pvalb’, ‘Sst’, ‘Bdnf’, ‘Th’, ‘Slc17a7’.

  • product_id (integer) (optional) Product ID for the dataset type. 1=Mouse Brain ISH, 2=Mouse Brain microarray. Default: 1.

  • num_rows (integer) (optional) Max results to return. Default: 50.

Example Usage:

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

AllenBrain_get_structure (Type: AllenBrainTool)

Get detailed information about a brain structure by its Allen Brain Atlas structure ID. Returns f…

AllenBrain_get_structure tool specification

Tool Information:

  • Name: AllenBrain_get_structure

  • Type: AllenBrainTool

  • Description: Get detailed information about a brain structure by its Allen Brain Atlas structure ID. Returns full structure record including name, hierarchy path, parent structure, color code. Example: structure_id=382 returns ‘Field CA1’ in hippocampus.

Parameters:

  • structure_id (integer) (required) Allen Brain Atlas structure ID. Examples: 382 (CA1), 375 (Hippocampus), 315 (Isocortex), 997 (root).

Example Usage:

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

AllenBrain_get_structure_expression_values (Type: AllenBrainTool)

Get quantified per-structure gene-expression values (StructureUnionize) for one Allen Mouse Brain…

AllenBrain_get_structure_expression_values tool specification

Tool Information:

  • Name: AllenBrain_get_structure_expression_values

  • Type: AllenBrainTool

  • Description: Get quantified per-structure gene-expression values (StructureUnionize) for one Allen Mouse Brain ISH experiment (SectionDataSet). Returns the actual numeric spatial expression aggregated over each annotated brain structure: expression_energy (intensity x density), expression_density (fraction of expressing pixels), sum_expressing_pixels, plus the structure record (acronym, name). This is the real spatial expression signal, not just experiment metadata. Get a section_data_set_id from AllenBrain_get_expression_datasets. Example: section_data_set_id=75457539 (a Gad1 mouse-brain ISH dataset) returns 2406 per-structure rows.

Parameters:

  • section_data_set_id (integer) (required) Allen Brain Atlas SectionDataSet (ISH experiment) ID. Get one from AllenBrain_get_expression_datasets. Example: 75457539 (a Gad1 mouse-brain ISH dataset).

  • include_structure (boolean) (optional) Whether to include the linked brain structure record (acronym, name, hierarchy) for each row. Default: true.

  • num_rows (integer) (optional) Max per-structure rows to return. There are ~2400 structures per dataset. Default: 50.

Example Usage:

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

AllenBrain_search_genes (Type: AllenBrainTool)

Search for genes in the Allen Brain Atlas by gene symbol (acronym) or name. Returns gene metadata…

AllenBrain_search_genes tool specification

Tool Information:

  • Name: AllenBrain_search_genes

  • Type: AllenBrainTool

  • Description: Search for genes in the Allen Brain Atlas by gene symbol (acronym) or name. Returns gene metadata including Entrez ID, chromosome, homologene ID. Useful for finding gene IDs needed to query expression data. Example: ‘Gad1’ returns glutamate decarboxylase 1 records for mouse and rat.

Parameters:

  • gene_acronym ([‘string’, ‘null’]) (optional) Gene symbol/acronym for exact match. Examples: ‘Gad1’, ‘Pvalb’, ‘Sst’, ‘Bdnf’, ‘Th’.

  • gene_name ([‘string’, ‘null’]) (optional) Gene name for partial match search (alternative to gene_acronym). Example: ‘glutamate decarboxylase’.

  • num_rows (integer) (optional) Max results to return. Default: 50.

Example Usage:

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

AllenBrain_search_structures (Type: AllenBrainTool)

Search for brain structures/regions in the Allen Brain Atlas ontology by acronym or name. Returns…

AllenBrain_search_structures tool specification

Tool Information:

  • Name: AllenBrain_search_structures

  • Type: AllenBrainTool

  • Description: Search for brain structures/regions in the Allen Brain Atlas ontology by acronym or name. Returns structure hierarchy, atlas coordinates, and color coding. Example: ‘CA1’ returns hippocampal Field CA1 across multiple atlases.

Parameters:

  • acronym ([‘string’, ‘null’]) (optional) Structure acronym for exact match. Examples: ‘CA1’, ‘VISp’, ‘TH’, ‘HIP’, ‘CTX’.

  • name ([‘string’, ‘null’]) (optional) Structure name for partial match (alternative to acronym). Example: ‘hippocampus’, ‘cerebellum’.

  • num_rows (integer) (optional) Max results to return. Default: 50.

Example Usage:

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