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

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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.
  • Install uv and use a computer with a display for napari.
  • Have a WaveOrder reconstruction config, such as one the WaveOrder tutorial 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.

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Run the Skill

Show the transfer function for a config

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.

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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.

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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.

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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.

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Skill files