> ## 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.

# Visualize a WaveOrder transfer function

> Use the Biohub MCP waveorder-visualize-otf Skill to compute the transfer function of a WaveOrder reconstruction config on your own computer and open it in napari.

Use `waveorder-visualize-otf` to see how a config's numerical aperture, wavelength, and pixel size shape its transfer function before you reconstruct.

> [!NOTE]
>
> This Skill calls no Biohub tools, so none of your data reaches Biohub.
> Your AI client runs the `wo` command and napari on your own computer.

## Before you begin

* Connect Biohub MCP to a client that can run commands on your computer, such as Claude Code, Codex, or Cursor; see [Connect your client](/biohub-mcp/connect-clients.md).
* Install [uv](https://docs.astral.sh/uv/) and use a computer with a display for napari.
* Have a WaveOrder reconstruction config, such as one the [WaveOrder tutorial](/biohub-mcp/skills/waveorder-tutorial.md) wrote.
* Have one OME-Zarr position with your data's ZYX shape.
  The Skill reads only its shape, so any dataset of that shape works.

## Run the Skill

Show the transfer function for a config

Using the Biohub MCP waveorder-visualize-otf Skill, show me the transfer function for my config phase\_3d.yml using the data at data.zarr/0/0/0.

If your client answers without the Skill, ask it to read `skill://waveorder-visualize-otf/SKILL.md` and follow it, or see [The assistant ignores a Skill](/biohub-mcp/troubleshooting.md#the-assistant-ignores-a-skill).

## What the Skill guides

1. It asks for a reconstruction config and one OME-Zarr position.
2. It runs `wo compute-tf` to write the transfer function to `./<config>_otf.zarr`, so results for different configs sit side by side.
3. It opens the result with `wo view` without blocking the client.

To compare settings, give it several configs: it computes each transfer function and opens them all in one napari window.

## Expected result

The result includes:

* The path to `./<config>_otf.zarr`.
* A napari window with the real and imaginary parts of the transfer function, with DC at the center.
* For a 2D phase config, the absorption and phase transfer functions, which `wo view` rebuilds from the stored singular system.

## What runs on your computer

The Skill runs `wo compute-tf` and `wo view` in your working folder.
If `wo` isn't installed, it runs both through `uvx --from "waveorder[all]"` instead of installing WaveOrder.

## Skill files

| Resource | URI |
| - | - |
| Instructions | `skill://waveorder-visualize-otf/SKILL.md` |
| File list | `skill://waveorder-visualize-otf/_manifest` |
| License (BSD 3-Clause) | `skill://waveorder-visualize-otf/LICENSE.md` |

## Related documentation

* [Reconstruct microscopy data with WaveOrder](/biohub-mcp/skills/waveorder-tutorial.md)
* [Biohub MCP Skills](/biohub-mcp/skills/overview.md)
* [Skills that run commands on your computer](/biohub-mcp/security.md#skills-that-run-commands-on-your-computer)
* [WaveOrder on GitHub](https://github.com/mehta-lab/waveorder)