> ## Documentation Index
> Fetch the complete documentation index at: https://docs.biohub.ai/llms.txt
> Use this file to discover all available pages before exploring further.

# Biohub MCP Skills

> Biohub MCP Skills are step-by-step instructions your AI client reads from the server and follows on your computer, such as a guided WaveOrder microscopy reconstruction.

A Skill is a set of instructions, with any supporting files and scripts, that your AI client reads from Biohub MCP and follows step by step.
Biohub MCP serves a Skill's files as text and never runs them.
Any command a Skill asks for runs wherever your client runs it, usually your own computer.
Like the rest of Biohub MCP, Skills need no sign-in.

## Choose a Skill

### WaveOrder

WaveOrder is an open-source package from the Mehta Lab at Biohub that makes physics-based reconstructions of label-free and fluorescence microscopy data.
Its source code and examples are on [GitHub](https://github.com/mehta-lab/waveorder).

> **[Reconstruct microscopy data](/biohub-mcp/skills/waveorder-tutorial.md)**
>
> Go from a raw stack or a sample dataset to a tuned reconstruction config.

> **[Visualize a transfer function](/biohub-mcp/skills/waveorder-visualize-otf.md)**
>
> Compute a config's transfer function and inspect it in napari.

## What your client needs

The WaveOrder Skills call no Biohub tools.
They need a client that can run commands on your computer, such as Claude Code, Codex, or Cursor, with [uv](https://docs.astral.sh/uv/) installed and a display for napari.
A chat-only client can read these Skills but can't follow them.
Review each command before you approve it, as [Security and privacy](/biohub-mcp/security.md#skills-that-run-commands-on-your-computer) explains.

## Start a Skill

Ask for the task and name the Skill, such as "Using the Biohub MCP waveorder-tutorial Skill, ...".
When a request matches a Skill, the server's instructions tell your client to read that Skill's `SKILL.md` first.
A client that can't read MCP resources can call [`read_resource`](/biohub-mcp/resource-tools#read-resource) with the `SKILL.md` URI, such as `skill://waveorder-tutorial/SKILL.md`, and [`list_resources`](/biohub-mcp/resource-tools#list-resources) to see every Skill file.
Some clients, such as Codex, ask you to approve `read_resource` first.
If your client answers without the Skill, see [The assistant ignores a Skill](/biohub-mcp/troubleshooting.md#the-assistant-ignores-a-skill).

## Files and versions

Every Skill serves these resources under `skill://<name>/`:

| Resource | What it holds |
| - | - |
| `SKILL.md` | The instructions your client follows. |
| `_manifest` | Every file the Skill serves, with its size and SHA-256 hash. |
| Supporting files | Any reference files, scripts, and license the Skill ships. `SKILL.md` tells your client when to read each one. |

Each Skill resource also carries the Skill's version and every file's size and SHA-256 hash in its MCP `_meta`, under `biohub.ai/skill-provenance`.
Use that live metadata, not a value copied from these docs, when you need the exact deployed version.

## Next steps

* Set up a client that can run commands with [Connect your client](/biohub-mcp/connect-clients.md).
* Start with [Reconstruct microscopy data with WaveOrder](/biohub-mcp/skills/waveorder-tutorial.md).