Neuromorpho Tools

Configuration File: neuromorpho_tools.json Tool Type: Local Tools Count: 7

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

Available Tools

NeuroMorpho_get_field_values (Type: NeuroMorphoTool)

Get available values for a neuron metadata field in NeuroMorpho.Org. Useful for discovering what …

NeuroMorpho_get_field_values tool specification

Tool Information:

  • Name: NeuroMorpho_get_field_values

  • Type: NeuroMorphoTool

  • Description: Get available values for a neuron metadata field in NeuroMorpho.Org. Useful for discovering what species, brain regions, cell types, or other attributes are available for searching. Example: field_name=’species’ returns all species represented in the database.

Parameters:

  • field_name (string) (required) Metadata field name. Common fields: ‘species’, ‘brain_region’, ‘cell_type’, ‘archive’, ‘stain’, ‘protocol’, ‘gender’, ‘age_classification’, ‘experiment_condition’.

  • page (integer) (optional) Page number (0-indexed). Default: 0.

  • size (integer) (optional) Results per page (max 500). Default: 500.

Example Usage:

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

NeuroMorpho_get_literature (Type: NeuroMorphoTool)

Get a single source-publication (literature) record by its NeuroMorpho article_id. Returns the fu…

NeuroMorpho_get_literature tool specification

Tool Information:

  • Name: NeuroMorpho_get_literature

  • Type: NeuroMorphoTool

  • Description: Get a single source-publication (literature) record by its NeuroMorpho article_id. Returns the full record: DOI, PMID, journal, title, authors, plus the species, brainRegion, cellType, and tracingSystem of the linked reconstructions. Get an article_id from NeuroMorpho_search_literature. Example: article_id=’56e9c892e4b0355017b2fa0f’ returns DOI 10.1023/A:1005260824715, journal ‘Neurophysiology’, species [‘frog’], brainRegion [‘Motor cortex’].

Parameters:

  • article_id (string) (required) NeuroMorpho internal article ID from NeuroMorpho_search_literature. Example: ‘56e9c892e4b0355017b2fa0f’.

Example Usage:

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

NeuroMorpho_get_morphometry (Type: NeuroMorphoTool)

Get morphometric measurements for a neuron from NeuroMorpho.Org. Returns quantitative properties …

NeuroMorpho_get_morphometry tool specification

Tool Information:

  • Name: NeuroMorpho_get_morphometry

  • Type: NeuroMorphoTool

  • Description: Get morphometric measurements for a neuron from NeuroMorpho.Org. Returns quantitative properties including surface area, volume, number of stems, bifurcations, branches, width, height, depth, average diameter, Euclidean/path distance, fractal dimension, and more.

Parameters:

  • neuron_id ([‘integer’, ‘null’]) (optional) Numeric neuron ID. Example: 1.

  • neuron_name ([‘string’, ‘null’]) (optional) Neuron name (alternative to neuron_id). Example: ‘cnic_001’.

Example Usage:

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

NeuroMorpho_get_neuron (Type: NeuroMorphoTool)

Get detailed neuron reconstruction data from NeuroMorpho.Org by neuron ID or name. Returns specie…

NeuroMorpho_get_neuron tool specification

Tool Information:

  • Name: NeuroMorpho_get_neuron

  • Type: NeuroMorphoTool

  • Description: Get detailed neuron reconstruction data from NeuroMorpho.Org by neuron ID or name. Returns species, brain region, cell type, staining method, reconstruction software, morphological attributes, and associated publications. Example: neuron_id=1 returns a Rhesus monkey prefrontal pyramidal neuron.

Parameters:

  • neuron_id ([‘integer’, ‘null’]) (optional) Numeric neuron ID in NeuroMorpho.Org database. Examples: 1, 102399, 50000.

  • neuron_name ([‘string’, ‘null’]) (optional) Neuron name string (alternative to neuron_id). Example: ‘cnic_001’.

Example Usage:

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

NeuroMorpho_get_persistence_vector (Type: NeuroMorphoTool)

Get the persistence vector (Topological Morphology Descriptor, TMD) for a NeuroMorpho neuron by i…

NeuroMorpho_get_persistence_vector tool specification

Tool Information:

  • Name: NeuroMorpho_get_persistence_vector

  • Type: NeuroMorphoTool

  • Description: Get the persistence vector (Topological Morphology Descriptor, TMD) for a NeuroMorpho neuron by its numeric neuron_id. Returns a 100-coefficient shape signature plus a scaling_factor, used as a feature vector for ML clustering and classification of dendritic/neuronal morphology. Get a neuron_id from NeuroMorpho_search_neurons or NeuroMorpho_get_neuron. Example: neuron_id=1 returns scaling_factor 244.928 and a 100-element coefficients array (3276.79, 3356.89, …).

Parameters:

  • neuron_id (integer) (required) NeuroMorpho numeric neuron ID. Get one from NeuroMorpho_search_neurons. Example: 1.

Example Usage:

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

NeuroMorpho_search_literature (Type: NeuroMorphoTool)

Search source-publication (literature) records linked to NeuroMorpho neuron reconstructions, sear…

NeuroMorpho_search_literature tool specification

Tool Information:

  • Name: NeuroMorpho_search_literature

  • Type: NeuroMorphoTool

  • Description: Search source-publication (literature) records linked to NeuroMorpho neuron reconstructions, searchable by neuroscience-specific fields. Each record gives DOI, PMID, journal, title, authors, plus the species, brainRegion, cellType, and tracingSystem of the reconstructions described. Use this to find the publications behind morphologies for a given brain region or cell type. Example: query_field=’brainRegion’, query_value=’hippocampus’ returns 128 articles (e.g. DOI 10.1084/jem.20151776).

Parameters:

  • query_field (string) (optional) Field to search. Neuroscience-specific options: ‘brainRegion’, ‘cellType’, ‘tracingSystem’, ‘species’. Also: ‘journal’, ‘doi’, ‘pmid’, ‘authors’, ‘title’. Default: ‘brainRegion’.

  • query_value (string) (required) Value to match for the chosen field. Examples: ‘hippocampus’ (brainRegion), ‘pyramidal’ (cellType), ‘mouse’ (species), ‘Neurolucida’ (tracingSystem).

  • page ([‘integer’, ‘null’]) (optional) Page number for pagination (0-indexed). Default: 0.

  • size ([‘integer’, ‘null’]) (optional) Number of articles per page (max 500). Default: 20.

Example Usage:

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

NeuroMorpho_search_neurons (Type: NeuroMorphoTool)

Search for neurons in NeuroMorpho.Org by species, brain region, cell type, or other attributes. S…

NeuroMorpho_search_neurons tool specification

Tool Information:

  • Name: NeuroMorpho_search_neurons

  • Type: NeuroMorphoTool

  • Description: Search for neurons in NeuroMorpho.Org by species, brain region, cell type, or other attributes. Supports filtering by multiple criteria. Returns paginated list of matching neurons. Example: searching species ‘human’ returns thousands of human neuron reconstructions.

Parameters:

  • query_field (string) (optional) Field to search on. Common fields: ‘species’, ‘brain_region’, ‘cell_type’, ‘archive’, ‘stain’, ‘protocol’. Use NeuroMorpho_get_field_values to see available values.

  • query_value (string) (required) Value to search for. Examples: ‘human’, ‘rat’, ‘mouse’, ‘hippocampus’, ‘pyramidal’, ‘interneuron’. Comma-separated for multiple values.

  • filter_field ([‘string’, ‘null’]) (optional) Optional additional filter field. Example: ‘cell_type’.

  • filter_value ([‘string’, ‘null’]) (optional) Value for the filter field. Example: ‘pyramidal’.

  • page (integer) (optional) Page number (0-indexed). Default: 0.

  • size (integer) (optional) Results per page (max 500). Default: 20.

Example Usage:

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