Napari MCP Server
Allows OpenAI LLMs (e.g., GPT-4) to remotely control napari viewers for microscopy image analysis.
Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@Napari MCP ServerLoad image from data/sample.tif and apply viridis colormap"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
Napari MCP Server
MCP server for remote control of napari viewers via Model Context Protocol (MCP). Perfect for AI-assisted microscopy analysis with Claude Desktop and other LLM applications.
https://github.com/user-attachments/assets/d261674c-9875-4671-8c60-a7f49d6f1b84
๐ Quick Start (3 Steps)
1. Install the Package
pip install napari-mcp2. Auto-Configure Your AI Application
# For Claude Desktop
napari-mcp-install install claude-desktop
# Include a napari GUI backend in the uv environment
napari-mcp-install install claude-desktop --backend pyqt6
# For other applications (Claude Code, Cursor, Cline, etc.)
napari-mcp-install install --help # See all options3. Restart Your Application & Start Using
Restart your AI app and you're ready! Try asking:
"Can you call session_information() to show my napari session details?"โ See Full Documentation for detailed guides
Related MCP server: Gemini MCP Server
๐ Using as a napari Plugin
napari-mcp can also be used as a napari plugin for direct integration with a running napari session:
Start napari normally:
napariOpen the widget: Plugins โ napari-mcp: MCP Server Control
Click "Start Server" to expose your current session to AI assistants
Connect your AI app using the standard installer:
napari-mcp-install install <app>
This mode enables AI assistants to control your current napari session rather than starting a new viewer. Perfect for integrating with existing workflows!
โ See Plugin Guide for detailed instructions
๐ฏ What Can You Do?
Basic Image Analysis
"Load the image from ./data/sample.tif and apply a viridis colormap"
"Create point annotations at coordinates [[100,100], [200,200]]"
"Take a screenshot and save it"Advanced Workflows
"Execute this code to create a filtered version:
from scipy import ndimage
filtered = ndimage.gaussian_filter(viewer.layers[0].data, sigma=2)
viewer.add_image(filtered, name='filtered')"
"Install scikit-image and segment the cells in this microscopy image"3D/4D Navigation
"Switch to 3D display mode"
"Navigate to time point 5, Z-slice 10"
"Create a rotating animation of this volume"Automated Workflows
Want to automate image processing with Python scripts? Use any LLM (OpenAI, Anthropic, etc.) with napari MCP:
โ See Python Integration Examples for batch processing and workflow automation
๐ค Supported AI Applications
Application | Command | Status |
Claude Desktop |
| โ Full Support |
Claude Code |
| โ Full Support |
Cursor IDE |
| โ Full Support |
Cline (VS Code) |
| โ Full Support |
Cline (Cursor) |
| โ Full Support |
Gemini CLI |
| โ Full Support |
Codex CLI |
| โ Full Support |
โ See Integration Guides for application-specific instructions
๐ Available MCP Tools
The server exposes 16 tools for complete napari control:
Core Functions
Session Management:
init_viewer,close_viewer,session_informationLayer Operations:
add_layer,list_layers,get_layer,remove_layer,set_layer_properties,reorder_layer,apply_to_layers,save_layer_dataViewer Controls:
configure_viewerUtilities:
screenshot,execute_code,install_packages,read_output
โ ๏ธ Security Notice
!!! warning "Code Execution Capabilities" This server includes powerful tools that allow arbitrary code execution:
- **`execute_code()`** - Runs Python code in the server environment
- **`install_packages()`** - Installs packages via pip
The bridge server binds to `127.0.0.1` (localhost only) with no authentication.
Any local process can invoke these tools.
**Use only with trusted AI assistants on local networks.**
Never expose to public internet without proper sandboxing.๐ Documentation
Quick Start Guide - Get running in 3 minutes
Installation Options - Advanced installation methods
Integration Guides - Setup for specific AI applications
Python Examples - Automate workflows with custom scripts
Troubleshooting - Common issues and solutions
API Reference - Complete tool documentation
๐งช Development Setup
# Clone repository
git clone https://github.com/royerlab/napari-mcp.git
cd napari-mcp
# Install with development dependencies
pip install -e ".[dev]"
# Run tests
pytest -m "not realgui" # Skip GUI tests
pytest --cov=src --cov-report=html # With coverage๐ค Contributing
Contributions are welcome! Please:
Fork the repository
Create a feature branch (
git checkout -b feature/amazing-feature)Make your changes with tests
Run pre-commit hooks:
pre-commit run --all-filesCommit changes (
git commit -m 'Add amazing feature')Push to branch (
git push origin feature/amazing-feature)Open a Pull Request
๐ Architecture
state.pyโServerStateholding all mutable state (viewer, locks, execution namespace)server.pyโcreate_server(state)factory; tools defined as closures over stateqt_helpers.pyโ Qt application and viewer lifecycle managementoutput.pyโ Output truncation utilitybridge_server.pyโ Plugin bridge server (overrides 3 tools for Qt thread safety)viewer_protocol.pyโViewerProtocolfor typed viewer backendscli/โnapari-mcp-installCLI for configuring AI applications
Key features:
Thread-safe: All napari operations are serialized
Non-blocking: Qt event loop runs asynchronously
Stateful: Maintains viewer state across tool calls
Extensible: Easy to add new tools
๐ Resources
napari - Multi-dimensional image viewer
Model Context Protocol - MCP specification
FastMCP - Python MCP framework
Claude Desktop - AI assistant with MCP support
๐ License
BSD-3-Clause License - see LICENSE file for details.
๐ Acknowledgments
napari team for the excellent imaging platform
FastMCP for the MCP framework
Anthropic for Claude and MCP development
astral-sh for uv dependency management
Built with โค๏ธ for the microscopy and AI communities
Available Tools
16 toolsadd_layerA
Add a layer to the viewer.
Parameters
layer_type : str
One of: "image", "labels", "points", "shapes",
"vectors", "tracks", "surface".
path : str, optional
File path (for image/labels).
data : list, optional
Inline data (coordinates, shape vertices, etc.).
data_var : str, optional
Name of a variable in the execute_code namespace.
name : str, optional
Layer name. Defaults to variable name or filename.
colormap : str, optional
Colormap name (image only).
blending : str, optional
Blending mode (image only).
channel_axis : int, optional
Channel axis (image only).
size : float, optional
Point size in pixels (points only, default 10).
shape_type : str, optional
Shape type: "rectangle", "ellipse", "line", "path", "polygon"
(shapes only, default "rectangle").
edge_color : str, optional
Edge color (shapes/vectors only).
face_color : str, optional
Face color (shapes only).
edge_width : float, optional
Edge width in pixels (shapes/vectors only).
| Name | Required | Description | Default |
|---|---|---|---|
| layer_type | Yes | ||
| path | No | ||
| data | No | ||
| data_var | No | ||
| name | No | ||
| colormap | No | ||
| blending | No | ||
| channel_axis | No | ||
| size | No | ||
| shape_type | No | ||
| edge_color | No | ||
| face_color | No | ||
| edge_width | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description must carry the transparency burden. It reveals the tool is a mutation (adds layers) and details parameter behaviors, but it does not explicitly state side effects (e.g., whether it stacks layers, requires viewer initialization, or has order dependencies).
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Well-structured with a one-line purpose followed by a clear bullet-style parameter list. While lengthy due to 13 parameters, every item adds value and is front-loaded. Some redundancy could be trimmed (e.g., repeating defaults).
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Parameter documentation is thorough, but missing high-level context such as when to use, prerequisites (e.g., viewer must be initialized), or expected output behavior. The output schema exists but is not referenced; description could briefly mention return type.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Despite 0% schema coverage, the description provides exhaustive parameter details: allowed values, defaults, and context for each parameter (e.g., layer_type enums, colormap caveat 'image only', shape_type options). This far surpasses the baseline compensation needed.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states 'Add a layer to the viewer' with a specific verb and resource. It distinguishes from sibling tools like remove_layer, set_layer_properties, and list_layers, making the purpose unambiguous.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance on when to use this tool versus alternatives (e.g., init_viewer, set_layer_properties). The description only lists parameters without context on prerequisites or typical use cases.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
apply_to_layersA
Apply property changes to multiple layers matching a filter.
Parameters
filter_type : str, optional
Layer type name to match (e.g., "Image", "Labels", "Points").
filter_pattern : str, optional
Glob pattern matched against layer names (e.g., "seg_*").
properties : dict, optional
Properties to set on matched layers. Supported keys: visible,
opacity, colormap, blending, contrast_limits,
gamma, new_name (renames by appending a suffix is NOT
supported โ use set_layer_properties individually).
| Name | Required | Description | Default |
|---|---|---|---|
| filter_type | No | ||
| filter_pattern | No | ||
| properties | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The description discloses supported properties (visible, opacity, colormap, etc.) and a crucial limitation: renaming via suffix is NOT supported. This helps the agent understand the tool's capability and avoids unexpected failures. Since no annotations are provided, the description carries the full burden, and it does well in revealing constraints.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is structured with a concise opening sentence followed by a clear parameter list. It is informative without being overly verbose. A minor point is that it could be slightly more compact, but the level of detail is appropriate given the lack of schema descriptions.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's complexity (3 optional parameters) and the presence of an output schema, the description adequately covers the tool's purpose, parameters, and a key limitation. It does not mention what happens when no layers match or error conditions, but these may be covered by the output schema. Overall, it provides sufficient context for correct invocation.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 0%, so the description fully explains each parameter: filter_type (layer type name like 'Image'), filter_pattern (glob pattern like 'seg_*'), and properties (dict with specific keys and examples). This adds significant meaning beyond the schema's minimal title fields, enabling proper usage.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool applies property changes to multiple layers matching a filter. It specifies the action (apply), the resource (property changes), the target (multiple layers), and the selection mechanism (filter). This purpose distinguishes it from siblings like set_layer_properties, which is for individual layer operations.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides guidance on when not to use this tool: it states that renaming by appending a suffix is not supported and directs to use set_layer_properties individually for that. This implicitly tells the agent to use this tool for bulk property changes other than suffix renaming. However, it does not explicitly list all alternative tools or scenarios.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
close_viewerA
Close the viewer window and clear all layers.
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description must disclose behavior. It states that closing the viewer also clears all layers, which is useful. However, it does not mention side effects like unsaved data or whether the operation is reversible.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single sentence of 8 words, containing no fluff. Every word adds value, and it is front-loaded with the main action.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's simplicity (no parameters, clear action) and the presence of an output schema (not shown but exists), the description is largely complete. It could benefit from mentioning any state dependencies, but overall it covers the essential context.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
There are zero parameters, and schema coverage is 100%. According to the rules, baseline for 0 parameters is 4. The description appropriately adds no parameter details since none exist.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description uses a specific verb (close) with a clear resource (viewer window) and adds the action of clearing all layers. It clearly distinguishes from sibling tools like init_viewer and configure_viewer.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance is provided on when to use this tool versus alternatives. There is no mention of prerequisites, such as requiring the viewer to be open, or comparisons with other tools.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
configure_viewerA
Configure viewer display: camera, dimensions, and grid.
All parameters are optional โ set any combination in one call.
Parameters
reset_view : bool, default False
If True, reset the camera to fit all data.
center : list[float], optional
Camera center position.
zoom : float, optional
Camera zoom factor (must be > 0).
angles : list[float], optional
Camera angles as [azimuth, elevation, roll] in degrees.
ndisplay : int, optional
Number of displayed dimensions (2 or 3).
dims_axis : int, optional
Axis index for slider position (use with dims_value).
dims_value : int, optional
Step value for the given axis.
grid : bool, optional
Enable or disable grid view.
| Name | Required | Description | Default |
|---|---|---|---|
| reset_view | No | ||
| center | No | ||
| zoom | No | ||
| angles | No | ||
| ndisplay | No | ||
| dims_axis | No | ||
| dims_value | No | ||
| grid | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations provided, so description bears full burden. It explains each parameter's effect (e.g., reset_view resets camera to fit data, zoom must be >0). Does not disclose persistence or side effects, but is fairly transparent.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Concise: one-line header, note on optionality, then structured list of parameters. Every sentence is useful and front-loaded with purpose.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Covers all parameters well. Output schema exists, so no need for return value details. Missing context about which viewer is affected (likely active viewer), but otherwise complete.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
With 0% schema description coverage, the description fully compensates by detailing all 8 parameters with types, defaults, and meanings. Adds significant value beyond raw schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Description clearly states 'Configure viewer display: camera, dimensions, and grid.' It uses a specific verb-resource pair and distinguishes from siblings like init_viewer or add_layer.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicitly notes that all parameters are optional and can be set in one call. Provides clear usage context but does not mention when not to use or alternatives.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
execute_codeA
Execute arbitrary Python code in the server's interpreter.
Similar to napari's console. The execution namespace persists across calls and includes 'viewer', 'napari', and 'np'.
Parameters
code : str Python code string. The value of the last expression (if any) is returned as 'result_repr'. line_limit : int, default=30 Maximum number of output lines to return. Use -1 for unlimited output. Warning: Using -1 may consume a large number of tokens.
Note
In standalone mode, code execution runs synchronously on the main thread (required for Qt/napari operations) and has no timeout. In bridge mode, a 600-second timeout is enforced.
| Name | Required | Description | Default |
|---|---|---|---|
| code | Yes | ||
| line_limit | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations provided, so description fully covers behavior: namespace persistence, included objects, return value, and mode-dependent execution details (synchronous, timeout).
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Description is well-structured with sections, efficient sentences, and no unnecessary words. Every sentence contributes value.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given moderate complexity, the description covers execution behavior, namespace, return value, and mode differences, making it fully adequate for informed use.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
With 0% schema description coverage, the description explains both parameters (code and line_limit) with default values and warnings, adding significant value beyond schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states 'Execute arbitrary Python code in the server's interpreter.' and distinguishes from siblings by mentioning similarity to napari's console and persistent namespace.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies usage for code execution but does not explicitly state when to use this tool vs alternatives or provide exclusions.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
get_layerA
Get detailed info about a layer, optionally including data.
Always returns metadata (shape, dtype, scale, translate, type-specific
properties). When include_data=True or slicing is provided,
also returns statistics and/or raw data values.
Parameters
name : str
Layer name (exact match).
include_data : bool, default False
If True, include data statistics (min/max/mean/std) and, for
small layers, inline data values.
slicing : str, optional
Numpy-style index string, e.g. "0, :5, :5". Implies
include_data=True.
max_elements : int, default 1000
Maximum number of data elements to return inline. Larger data
is stored and an output_id returned for read_output.
| Name | Required | Description | Default |
|---|---|---|---|
| name | Yes | ||
| include_data | No | ||
| slicing | No | ||
| max_elements | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description carries full burden. It discloses that metadata is always returned, and data statistics/inline values are included when include_data or slicing is provided. It also mentions that large data returns an output_id for use with read_output. This is good behavioral disclosure, though it omits error behavior (e.g., invalid name).
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is concise and well-structured: a summary sentence followed by a clear parameter list. Every sentence adds value, and the format is easy to parse. It is appropriately sized for the tool.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the complexity (4 parameters, output schema exists), the description covers input semantics well. It mentions expected output fields (shape, dtype, etc.) but does not detail the output schema structure (though output schema exists). The description is complete enough for an AI agent to use correctly.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Despite 0% schema description coverage, the description provides detailed parameter semantics: name (exact match), include_data (controls statistics and inline values), slicing (numpy-style index, implies include_data), and max_elements (threshold for inline vs stored data). This adds significant meaning beyond the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states 'Get detailed info about a layer, optionally including data.' This is a specific verb+resource that distinguishes it from siblings like list_layers (list all) and read_output (retrieve stored data). The purpose is unambiguous.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description does not guide when to use this tool versus alternatives like list_layers or read_output. It explains parameters but lacks context for choosing between get_layer and sibling tools. No explicit when-to-use or when-not-to-use guidance.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
init_viewerA
Create or return the napari viewer, with viewer detection.
When detect_only=True, reports available viewers (local and
external) without creating or modifying anything.
Parameters
title : str, optional Optional window title (only for local viewer). width : int, optional Optional initial canvas width (only for local viewer). height : int, optional Optional initial canvas height (only for local viewer). port : int, optional If provided, attempt to connect to an external napari-mcp bridge on this port (default is taken from NAPARI_MCP_BRIDGE_PORT or 9999). detect_only : bool, default=False If True, only detect available viewers without initialising.
| Name | Required | Description | Default |
|---|---|---|---|
| title | No | ||
| width | No | ||
| height | No | ||
| port | No | ||
| detect_only | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description must fully disclose behavioral traits. It clarifies that detect_only=True reports viewers without initializing, and mentions port for external bridge. However, it does not describe what 'return' means (return value) or any side effects like viewer display state.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is front-loaded with the main purpose and includes a well-organized parameter section. However, the parameter documentation is somewhat verbose; each parameter's explanation could be more concise.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given 5 parameters and no annotations, the description covers parameters comprehensively. However, it omits explanation of the return value despite an output schema existing, leaving a gap in completeness.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%, but the description includes detailed parameter documentation (title, width, height, port, detect_only) explaining their purpose and defaults. This adds significant meaning beyond the bare schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states 'Create or return the napari viewer, with viewer detection.' It uses specific verbs and a distinct resource, differentiating from siblings like close_viewer or configure_viewer.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explains the detect_only mode and its use case, providing context on when to use this tool without creating a viewer. However, it does not explicitly contrast with sibling tools like close_viewer or configure_viewer.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
install_packagesA
Install Python packages using pip.
Parameters
packages : list of str List of package specifiers (e.g., "scikit-image", "torch==2.3.1"). upgrade : bool, optional If True, pass --upgrade flag. no_deps : bool, optional If True, pass --no-deps flag. index_url : str, optional Custom index URL. extra_index_url : str, optional Extra index URL. pre : bool, optional Allow pre-releases (--pre flag). line_limit : int, default=30 Maximum number of output lines to return. Use -1 for unlimited output. timeout : int, default=240 Timeout for pip install in seconds.
| Name | Required | Description | Default |
|---|---|---|---|
| packages | Yes | ||
| upgrade | No | ||
| no_deps | No | ||
| index_url | No | ||
| extra_index_url | No | ||
| pre | No | ||
| line_limit | No | ||
| timeout | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The description details parameters like upgrade and no_deps, which hint at side effects, but it does not explicitly state that the tool modifies the Python environment, requires network access, or may have other behavioral traits. With no annotations, this is adequate but not thorough.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is front-loaded with a clear purpose statement and uses a clean parameters section. It is structured well but slightly verbose, with each parameter having a full sentence. It earns its place but could be more concise.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool has 8 parameters and an output schema (not shown), the description covers parameter semantics well but lacks behavioral context such as prerequisites, side effects, or error scenarios. It is sufficient for basic use but incomplete for advanced understanding.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The input schema has 0% description coverage, so the description carries the full burden. It provides detailed explanations for all 8 parameters, including examples for packages, defaults, and flag mappings (e.g., '--upgrade flag'). This adds significant meaning beyond the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description begins with 'Install Python packages using pip,' clearly stating the action (install) and resource (Python packages via pip). This is specific and distinguishes the tool from sibling tools that deal with viewer layers, code execution, etc.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides no guidance on when to use this tool versus alternatives, such as using execute_code for more flexible installation or other package managers. It only describes what the tool does.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
list_layersC
Return a list of layers with key properties.
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
Output Schema
| Name | Required | Description |
|---|---|---|
| result | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations provided, and the description only states it returns a list. It does not disclose whether the operation is read-only, any side effects, authentication needs, or performance implications.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is extremely concise at one sentence, but it is front-loaded and to the point. However, it could be slightly more specific about 'key properties'.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool has no parameters and an output schema exists, the description is minimally complete, but it lacks context about the scope of layers (e.g., from current viewer).
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The tool has no parameters, and the schema description coverage is 100%. The description adds no additional parameter semantics beyond what the schema provides, which is acceptable baseline.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states it returns a list of layers with key properties. However, it does not explicitly differentiate from sibling tools like 'get_layer' which returns a single layer, though the distinction is implicit.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance on when to use this tool versus alternatives such as 'get_layer' or 'add_layer'. The description fails to provide context for appropriate usage.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
read_outputA
Read stored tool output with optional line range.
Parameters
output_id : str Unique ID of the stored output. start : int, default=0 Starting line number (0-indexed). end : int, default=-1 Ending line number (exclusive). If -1, read to end.
| Name | Required | Description | Default |
|---|---|---|---|
| output_id | Yes | ||
| start | No | ||
| end | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description carries the full burden. It discloses the read operation and line range, but does not mention idempotency, caching, or any side effects. The basic behavior is clear, but no additional traits are described.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is concise with a single-sentence purpose followed by a clear parameter list. It is well-structured and front-loaded, though the parameter descriptions could be slightly more compact.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the existence of an output schema (not shown), the description adequately covers reading output with line range. It is complete for a read-only tool with three parameters, though it does not describe the return format.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The description explains each parameter's meaning and default values (output_id as unique ID, start as 0-indexed line number, end as exclusive with -1 for end). This adds value beyond the schema's minimal titles and types.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states 'Read stored tool output with optional line range,' which is a specific verb and resource. It distinguishes from sibling tools that deal with layers and viewers.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance on when to use this tool versus alternatives is provided. The description lacks context for appropriate usage scenarios.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
remove_layerC
Remove a layer by name.
| Name | Required | Description | Default |
|---|---|---|---|
| name | Yes |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description should fully disclose behavioral traits. It only states 'Remove a layer by name' without indicating if the removal is permanent, reversible, or has side effects on other layers. For a destructive operation, this is insufficient transparency.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is extremely concise with a single sentence, which is front-loaded. However, it is too minimalist for a tool with no additional details; conciseness here sacrifices usefulness.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
While an output schema exists (not shown), the description does not mention return values or the outcome of removal. Given the lack of annotations and parameter details, the description is incomplete for an agent to fully understand the tool's behavior.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The description adds no meaning beyond the input schema for the single parameter 'name'. Schema coverage is 0%, meaning the description must compensate, but it merely repeats parameter existence. No format or constraints are described.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the action 'Remove' and the resource 'layer by name'. It is specific and directly conveys the tool's function, distinguishing it from sibling tools like list_layers or set_layer_properties, though no explicit differentiation is provided.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
There is no guidance on when to use this tool versus alternatives like add_layer or apply_to_layers. The description lacks context on prerequisites, effects, or best practices, leaving the agent without clear decision-making support.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
reorder_layerA
Reorder a layer by name.
Provide exactly one of:
index: absolute target index
before: move before this layer name
after: move after this layer name
| Name | Required | Description | Default |
|---|---|---|---|
| name | Yes | ||
| index | No | ||
| before | No | ||
| after | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description must carry the burden. It does not disclose any behavioral traits such as side effects, reversibility, or triggers, only the mechanics of the parameters.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is short and front-loaded. It could be slightly more concise by merging the initial line with the parameter instructions, but it is efficient overall.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The tool has an output schema but the description does not mention the return format. It explains the parameter mutex well, but lacks context on what happens after reordering (e.g., confirmation, new order).
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%, but the description adds meaning by explaining that name identifies the layer and index, before, and after are mutually exclusive with specific semantics (absolute index vs. relative to layer name).
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states 'Reorder a layer by name,' specifying the verb and resource. It is distinct from sibling tools like add_layer, remove_layer, and list_layers.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description gives explicit instructions on using exactly one of index, before, or after. However, it does not provide guidance on when to use this tool versus alternatives like set_layer_properties.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
save_layer_dataA
Save a layer's data to a file.
Parameters
name : str
Layer name.
path : str
Output file path. Format is inferred from extension unless
format is specified. Supported: .tiff, .png,
.npy, .csv (points/tabular only).
format : str, optional
Explicit format override (e.g., "npy", "tiff").
| Name | Required | Description | Default |
|---|---|---|---|
| name | Yes | ||
| path | Yes | ||
| format | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description carries full responsibility. It describes the basic save operation but does not disclose if files are overwritten, required permissions, or error behavior. This is a significant gap.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is structured with a purpose sentence and parameter list, making it readable. It is slightly verbose with redundant formatting but still efficient.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The description covers the key functionality and parameter details. However, it lacks information on file overwrite behavior and error handling. Given that an output schema exists, return values are not needed, but behavioral completeness is only moderate.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 0%, so the description compensates well by explaining each parameter: name, path (with extension inference and supported formats), and format (optional override). Adds meaningful context beyond the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states it saves a layer's data to a file, with a specific verb and resource. It distinguishes from sibling tools like add_layer or remove_layer, implying saving to persistent storage.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explains the parameters and how format is inferred, but does not explicitly state when to use this tool over siblings or any prerequisites. It provides context for parameter usage.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
screenshotA
Take a screenshot, or a timelapse series by sweeping a dims axis.
For a single screenshot, call with no axis/slice_range.
For a timelapse, provide both axis and slice_range.
Parameters
canvas_only : bool, default True
If True, only capture the canvas area.
save_path : str, optional
Save single screenshot to this file path (returns metadata).
axis : int, optional
Dims axis to sweep for timelapse (e.g., temporal axis).
slice_range : str, optional
Python-like slice string, e.g. "1:5", ":6", "::2".
Required when axis is provided.
interpolate_to_fit : bool, default False
If True, downsample timelapse frames to fit ~1.3 MB total.
save_dir : str, optional
Save timelapse frames as frame_NNNN.png in this directory.
| Name | Required | Description | Default |
|---|---|---|---|
| canvas_only | No | ||
| save_path | No | ||
| axis | No | ||
| slice_range | No | ||
| interpolate_to_fit | No | ||
| save_dir | No |
Output Schema
| Name | Required | Description |
|---|---|---|
| result | Yes |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations provided, so description must disclose behavior. It explains the two modes, saving options, and interpolation limiting file size. However, it does not mention error handling, auth needs, or return format details (though output schema exists). The description is adequate but missing some behavioral context.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is concise and well-structured: a brief overall purpose, then a parameter list with detailed explanations. It front-loads the main functionality and each sentence adds value. No unnecessary fluff.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given 6 parameters, no annotations, and an output schema exists, the description covers the core functionality and parameter usage. It explains both modes and key options. However, it omits some edge cases (e.g., error if axis without slice_range) and does not reference the output schema for return values. Overall, fairly complete for an agent to use correctly.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
With 0% schema description coverage, the description does a good job explaining all 6 parameters: canvas_only, save_path, axis, slice_range, interpolate_to_fit, save_dir. It provides clear semantics, including slice string examples and interpolation purpose. However, it does not explain the anyOf types (e.g., string alternatives for boolean) and misses details on default return when no save_path given.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool's purpose: taking a screenshot or timelapse series. It distinguishes between two modes (single vs timelapse) with specific parameter guidance. The verb 'take' and resource 'screenshot' are precise, and no sibling tool has similar functionality.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides explicit usage guidance: when to use single screenshot (no axis/slice_range) vs timelapse (provide both). It explains parameters like canvas_only, save_path, and interpolation. However, it lacks explicit 'when not to use' or comparison to alternatives, though no similar siblings exist.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
session_informationA
Get comprehensive information about the current napari session.
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, and the description only says 'comprehensive information' without detailing what data is returned (e.g., viewer state, layer list, settings). The tool's read-only and non-destructive nature is implied but not explicitly stated.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Single sentence, no unnecessary words. Front-loaded with the key action and target.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Tool is simple with no parameters and an output schema exists to explain return values. However, the description is vague ('comprehensive information') and could be more specific about what session data is included, especially given the variety of sibling tools.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Tool has no parameters; the input schema is empty. Since schema coverage is 100% (no parameters to describe), baseline is 4. Description does not need to add parameter details.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Description clearly states 'Get comprehensive information about the current napari session', specifying a distinct verb and resource. This differentiates from sibling tools focused on layers, viewers, or code execution.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance on when to use this tool versus alternatives like get_layer or list_layers. The description does not provide context for appropriate invocation.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
set_layer_propertiesA
Set properties on a layer by name.
Parameters
name : str Layer name (exact match). visible, opacity, colormap, blending, contrast_limits, gamma Standard layer rendering properties. new_name : str, optional Rename the layer. active : bool, optional If True, make this the selected/active layer. Setting to False has no effect (use viewer selection directly).
| Name | Required | Description | Default |
|---|---|---|---|
| name | Yes | ||
| visible | No | ||
| opacity | No | ||
| colormap | No | ||
| blending | No | ||
| contrast_limits | No | ||
| gamma | No | ||
| new_name | No | ||
| active | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description must carry the full burden. It notes that setting active=False has no effect, but it does not disclose prerequisites (e.g., layer existence), side effects, or error behavior. This is insufficient for a mutation tool.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is concise, front-loaded with the main purpose, and well-structured with a 'Parameters' section. Every sentence adds value with no repetition or fluff.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's complexity (9 parameters, mutation), the description covers parameter semantics but omits return value description (though output schema exists), error handling, and preconditions like layer existence. It is adequate but has clear gaps.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
With 0% schema description coverage, the description compensates by explaining each parameter's purpose (e.g., 'Layer name (exact match)', 'Standard layer rendering properties', 'Rename the layer'). However, the explanation for rendering properties is vague, and exact accepted values (e.g., colormap names) are not given.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states 'Set properties on a layer by name,' identifying the verb (set) and resource (layer properties). It distinguishes from sibling tools like add_layer, get_layer, and remove_layer by focusing on modifying existing layers.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies usage for modifying layer properties but does not explicitly state when to use this tool versus alternatives. No exclusions or alternative tool names are provided.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Tool Schema Changelog
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
16 tool updates
v0.1.0- First observed
add_layer - First observed
apply_to_layers - First observed
close_viewer - First observed
configure_viewer - First observed
execute_code - First observed
get_layer - First observed
init_viewer - First observed
install_packages - First observed
list_layers - First observed
read_output - First observed
remove_layer - First observed
reorder_layer - First observed
save_layer_data - First observed
screenshot - First observed
session_information - First observed
set_layer_properties
TDQS
Scored across 16 tools
Each tool targets a distinct operation or query. Add/remove/reorder layers are clearly separate; set_layer_properties and apply_to_layers differ in scope; execute_code and read_output serve different purposes. No overlapping tools.
All tools use consistent snake_case with a verb_noun pattern (e.g., add_layer, list_layers, close_viewer). No mixed conventions or irregular naming.
16 tools is well-scoped for the napari viewer domain. Each tool serves a clear purpose without redundancy or unnecessary sprawl.
Core workflows (viewer lifecycle, layer manipulation, data I/O, code execution) are covered. Minor gaps exist, such as no dedicated file import for non-image layers, but these can be addressed via execute_code.
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