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segment_cells_batch

Segment cells in multiple images at once. Set image paths, model, diameter, GPU, and batch size to produce masks for all inputs.

Instructions

Segment cells in multiple images in batch.

Args: image_paths: List of paths to input images model_type: Cellpose model type diameter: Expected cell diameter in pixels output_dir: Directory to save masks (default: same as input images) gpu: Whether to use GPU acceleration batch_size: Number of images to process in parallel

Returns

Dictionary with batch processing results

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
gpuNo
diameterNo
batch_sizeNo
model_typeNocyto3
output_dirNo
image_pathsYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.1.5

TDQS

B3.4/5.0
Behavior2/5

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

With no annotations provided, the description carries the full burden of disclosing behavior. It mentions saving masks implicitly via the output_dir parameter but does not state that files will be written to disk, nor does it disclose GPU usage, potential side effects, or error behavior. The description is mostly a restatement of the parameter list, adding little beyond the schema.

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

Conciseness4/5

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

The description is concise, uses a clear list format for arguments, and includes a return type line. It is front-loaded with the core purpose and avoids fluff. Slightly more could be added about side effects, but the structure is efficient and scannable.

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

Completeness3/5

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

Given the tool's complexity (6 params, batch processing) and the presence of an output schema, the description is minimally adequate but lacks context on when to prefer this tool, error handling, resource requirements (e.g., GPU necessity), and what the returned dictionary contains. The output schema covers return structure, but overall context for safe and correct usage is incomplete.

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?

Schema description coverage is 0%, so the description must compensate. It does provide brief explanations for each parameter (e.g., 'image_paths: List of paths to input images'), adding meaning beyond the schema's type definitions. While not deeply detailed, it covers all six parameters and clarifies their purpose, meeting the compensation need.

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 states a specific verb-resource combination ('Segment cells in multiple images in batch') and clearly distinguishes from siblings like segment_cells_2d and segment_cells_3d by emphasizing batch processing. It is immediately obvious what the tool does and how it differs from single-image counterparts.

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

Usage Guidelines2/5

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

No explicit guidance is given on when to use this tool versus alternatives. The sibling names suggest single-image segmentation, but the description does not state 'use for multiple images' or 'for single images use segment_cells_2d/3d'. Context is implied by the word 'batch' but not stated as a decision rule.

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