Add waveorder-tutorial and visualize-otf-from-config Claude skills#569
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talonchandler wants to merge 3 commits into
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Add waveorder-tutorial and visualize-otf-from-config Claude skills#569talonchandler wants to merge 3 commits into
talonchandler wants to merge 3 commits into
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Interactive CLI walkthrough for a first reconstruction: environment check, OME-Zarr conversion, config authoring, napari viewing, and parameter sweeps. Includes a QPI 2D-from-defocus worked example using the zenodo recOrder_session sample. Un-ignores .claude/skills/ so the skill ships with the repo.
talonchandler
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July 16, 2026 18:57
Two-call skill: `wo compute-tf` on a config + input position, then `wo view` on the resulting transfer function (napari, backgrounded).
talonchandler
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For 2D reconstructions, the transfer function is stored as a singular system (U, S, Vh). `wo view` now reconstructs H = U @ diag(S) @ Vh at each lateral frequency and displays the resulting transfer function(s) — absorption and phase for 2D phase, the optical TF for 2D fluorescence — instead of the raw singular vectors. 3D display is unchanged.
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Adds two Claude Code skills under
.claude/skills/.waveorder-tutorial: walks a user through their firstwaveorderreconstruction over the CLI: environment check, OME-Zarr conversion, config authoring, napari viewing, and regularization sweeps.SKILL.md— the interactive step-by-step flowreferences/— conversion guide, config reference, and a ready-to-run QPI-2D configscripts/— example-data fetch, TIFF/array → OME-Zarr converter, and a parameter-sweep helpervisualize-otf-from-config: computes a transfer function (OTF) from a config and opens it in napari. Two calls:wo compute-tf -i <input>/0/0/0 -c <config> -o otf.zarr, thenwo view otf.zarr.How to trial
/waveorder-tutorial(or "try waveorder on my data") — with no data of your own, it fetches the QPI-defocus sample (recOrder_sessionfrom Zenodo) and reconstructs 2D phase from a defocus stack (config pre-filled inreferences/example_qpi_2d.yml). Bring your own TIFF/zarr/array to run the full convert → configure → reconstruct → sweep flow./visualize-otf-from-config <config.yml> <input.zarr>— computes the OTF for that config and opens it in napari.Results are shown interactively in napari (
wo view).