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 Allen Mouse Brain ISH expression datasets for a gene with exact RMA row pagination. Failed ex…

AllenBrain_get_expression_datasets tool specification

Tool Information:

  • Name: AllenBrain_get_expression_datasets

  • Type: AllenBrainTool

  • Description: Get Allen Mouse Brain ISH expression datasets for a gene with exact RMA row pagination. Failed experiments are excluded from data, while metadata separately reports the upstream total including failed rows, failed rows on this page, and next_start_row.

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) Results per page (1-2000).

  • start_row (integer) (optional) Zero-based RMA row offset. Continue with metadata.next_start_row.

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 StructureUnionize expression values for one Allen Mouse Brain ISH experiment. Each…

AllenBrain_get_structure_expression_values tool specification

Tool Information:

  • Name: AllenBrain_get_structure_expression_values

  • Type: AllenBrainTool

  • Description: Get quantified StructureUnionize expression values for one Allen Mouse Brain ISH experiment. Each dataset can contain about 2400 brain-structure rows; use start_row and follow metadata.next_start_row instead of treating the default 50-row page as complete. Returns expression_energy, expression_density, sum_expressing_pixels and optional structure records.

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) Per-structure rows per page (1-2000). There are approximately 2400 rows per dataset; continue with start_row.

  • start_row (integer) (optional) Zero-based RMA row offset. Continue with metadata.next_start_row.

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 Allen Brain Atlas genes by symbol or name with exact RMA row pagination. Metadata reports …

AllenBrain_search_genes tool specification

Tool Information:

  • Name: AllenBrain_search_genes

  • Type: AllenBrainTool

  • Description: Search Allen Brain Atlas genes by symbol or name with exact RMA row pagination. Metadata reports the upstream total and next_start_row so later gene matches remain reachable.

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) Results per page (1-2000).

  • start_row (integer) (optional) Zero-based RMA row offset. Continue with metadata.next_start_row.

Example Usage:

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

AllenBrain_search_structures (Type: AllenBrainTool)#

Search Allen Brain Atlas structures by acronym or name with exact RMA row pagination. Metadata re…

AllenBrain_search_structures tool specification

Tool Information:

  • Name: AllenBrain_search_structures

  • Type: AllenBrainTool

  • Description: Search Allen Brain Atlas structures by acronym or name with exact RMA row pagination. Metadata reports the upstream total and next_start_row so later structures remain reachable.

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) Results per page (1-2000).

  • start_row (integer) (optional) Zero-based RMA row offset. Continue with metadata.next_start_row.

Example Usage:

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