feat(default-reader): extract instrument-metadata block (objective + acquisition + channels) for OME-TIFF and other default-plugin formats — replaces #56

[ferrinm]

What to build

Broader-scope replacement for #56. Populate the full instrument-metadata surface on the catch-all default reader plugin path (src/zarrmony/readers/default.py), covering OME-TIFF and any other formats routed through the default bioio plugin (bioio-ome-tiff, bioio-tifffile, bioio-imageio, etc.).

Scope

For OME-TIFF and any format that already carries OME metadata, everything arrives pre-parsed via ome_types — the <Instrument>/<Objective> element and channel identity are likely already populated on the reader's ome_metadata. Propagate to:

1. Objective (originally feat(default-reader): extract objective lens metadata for OME-TIFF and other default-plugin formats #56): per_scene[i].objective — project from ome_metadata.instruments[0].objectives[...] when present, using the same field mapping as feat(lif): extract objective lens metadata (magnification, NA, immersion) into audit + OME-XML #52. Pass through OME-XML unchanged.
2. Acquisition + instrument (new from feat(lif): extract per-scene acquisition/instrument block (date, microscope, imaging_method) into audit + inspect #62): per_scene[i].acquisition — project from ome_metadata.images[i].acquisition_date and ome_metadata.instruments[0].microscope. Normalise imaging_method to the same token set.
3. Channels (from feat(audit): store per-scene channel identity (dye/fluor/excitation/emission) across all reader paths #61): project ome_metadata.images[0].pixels.channels into per_scene[i].channels with the ADR-locked shape.

For formats without native OME metadata (plain TIFF, PNG-like inputs), each block is simply omitted — no synthetic values, no warnings. Document in the PR description which of the default-plugin distributions expose which fields out of the box (extended from the #56 probe test).

Implementation notes

• Introspect reader.ome_metadata (or equivalent bioio surface) — if instruments[0]/images[i]/pixels.channels are populated, project into the same audit dict shape as the LIF path.
• Honour <Image>/<ObjectiveSettings> on the input OME so per-image objective linkage survives the round-trip.
• Reuse audit dict shape and OME-XML population helpers from feat(lif): extract objective lens metadata (magnification, NA, immersion) into audit + OME-XML #52 + feat(lif): extract per-scene acquisition/instrument block (date, microscope, imaging_method) into audit + inspect #62.
• Cross-format consistency check called out below — this is the plugin where inconsistencies between formats become most visible.

Acceptance criteria

• per_scene[i].objective, per_scene[i].acquisition, and per_scene[i].channels populated on an OME-TIFF fixture that has these elements in its input OME-XML.
• Blocks absent (no key, no null) on an input with no matching metadata.
• Output OME-XML preserves the input's <Objective> when present, or omits <Instrument> cleanly when not.
• Same blocks visible in inspect().scenes[i].
• Tests for both the "input has metadata" and "input has none" cases.
• PR description enumerates which default-plugin formats populate which blocks (extended from feat(default-reader): extract objective lens metadata for OME-TIFF and other default-plugin formats #56's original probe test; documented for future contributors and for the Aperture ingest team).
• Cross-format consistency check: field names + value types match LIF (feat(lif): extract objective lens metadata (magnification, NA, immersion) into audit + OME-XML #52 + feat(lif): extract per-scene acquisition/instrument block (date, microscope, imaging_method) into audit + inspect #62) exactly.
• CHANGELOG entry under a minor version bump.

Blocked by

• ADR-0007: Aperture BigQuery ↔ zarrmony field-mapping contract + instrument-metadata audit shape #60 (ADR-0007 locks the shape)
• feat(lif): extract per-scene acquisition/instrument block (date, microscope, imaging_method) into audit + inspect #62 (LIF establishes the acquisition/instrument block shape)
• feat(lif): extract objective lens metadata (magnification, NA, immersion) into audit + OME-XML #52 (LIF establishes the objective block + OME-XML injection helpers)

Replaces

• feat(default-reader): extract objective lens metadata for OME-TIFF and other default-plugin formats #56 (objective-only slice; closed in favor of this broader-scope reorg per the ingest-team mapping effort)