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load_data

Load spatial transcriptomics data from various formats (Visium, Xenium, etc.) and get a dataset with cell/gene counts and metadata for downstream analysis.

Instructions

Load spatial transcriptomics data with comprehensive metadata profile.

Args:
    data_path: Path to data file or directory
    data_type: 'visium', 'xenium', 'slide_seq', 'merfish', 'seqfish', or 'generic'
    name: Optional dataset name

Returns:
    SpatialDataset with cell/gene counts and metadata profiles

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
nameNo
data_pathYes
data_typeYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYes
nameYes
n_cellsNo
n_genesNo
uns_keysNo
data_typeYes
obsm_keysNo
descriptionNo
obs_columnsNo
var_columnsNo
top_expressed_genesNo
tissue_image_availableNo
top_highly_variable_genesNo
spatial_coordinates_availableNo
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=false and destructiveHint=false, so the safety profile is clear. The description adds that loading returns a SpatialDataset with cell/gene counts and metadata profiles, but does not disclose additional side effects or external access behavior beyond what annotations imply.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with Args and Returns sections, providing all necessary information in a compact and easily scannable format. No redundant or filler content.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the output schema and annotations, the description covers the essential aspects: loading data, supported data types, and return type. It doesn't address edge cases like error handling or file format details, but it is sufficient for a data loading tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The description's Args block explains all three parameters, including allowed values for data_type, which compensates for the schema's empty parameter descriptions (0% coverage). This adds meaningful context beyond the raw schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description uses a specific verb ('Load') and names the resource ('spatial transcriptomics data'), making it clear what the tool does. It is distinct from sibling tools like reload_data and preprocess_data, and the Args section further specifies data types and behaviors.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies this is the entry point for loading spatial data but does not explicitly state when to use it over reload_data or other alternatives. The data_type enum provides some context, but there is no when-to-use/when-not-to-use guidance or exclusions.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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