Lambda: Update arcadia-microscopy-tools to 0.4.1

[lanery]

Summary

• Bump arcadia-microscopy-tools to >=0.4.1 in lambda/pyproject.toml (+ regenerated uv.lock).
• Adapt the Hina ND2 pipeline to the breaking 0.4.0 API changes:
  • get_intensities_from_channel() → get_channel_intensities()
  • Channel.color is now a plain hex string (not an arcadia_pycolor.HexCode); serialize it directly, normalized to lowercase to keep the metadata JSON output stable.
• Update test_parse_metadata.py: replace the now-invalid Channel(color=None) case (color is a required, hex-validated string in 0.4.x) with a lowercase-normalization test.

Notes

• 0.4.0 also changed overlay blending to anchor the zero-point at transparent gray instead of transparent white, so generated composite JPGs will look slightly different even without code changes.

Test plan

• make check-all (format, lint, typecheck — Python + web)
• Validate the pipeline on a real ND2 file and visually sanity-check the composite overlay output

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Project	Deployment	Actions	Updated (UTC)
data-hub	Ready	Preview, Comment	Jun 9, 2026 6:08pm

[lanery]

Tested via CLI on an ND2 file with only one pre-defined channel (previously failed processing):

uv run data-hub-process hina "/Users/ryanlane/arc_nas_mirror/Hina/Tyler/2026/05/96_well_OilRedO/20260529_103039_362/WellB11_Channelred,green,blue,TRITC BP_Seq0002.nd2" --output-dir ./out

/Users/ryanlane/Repositories/data-hub/.venv/lib/python3.13/site-packages/arcadia_microscopy_tools/nikon.py:147: MetadataWarning: Optical configuration 'red' did not match a predefined channel; synthesizing a channel from ND2 metadata. Pass a Channel instance to prevent this warning.
  channel = self._build_fallback_channel(nd2_channel.channel)
/Users/ryanlane/Repositories/data-hub/.venv/lib/python3.13/site-packages/arcadia_microscopy_tools/nikon.py:147: MetadataWarning: Optical configuration 'green' did not match a predefined channel; synthesizing a channel from ND2 metadata. Pass a Channel instance to prevent this warning.
  channel = self._build_fallback_channel(nd2_channel.channel)
/Users/ryanlane/Repositories/data-hub/.venv/lib/python3.13/site-packages/arcadia_microscopy_tools/nikon.py:147: MetadataWarning: Optical configuration 'blue' did not match a predefined channel; synthesizing a channel from ND2 metadata. Pass a Channel instance to prevent this warning.
  channel = self._build_fallback_channel(nd2_channel.channel)
Exported JPG: out/WellB11_Channelred,green,blue,TRITC BP_Seq0002.jpg
{
  "sizes": {
    "Z": 9,
    "C": 4,
    "Y": 4263,
    "X": 4263
  },
  "channels": [
    {
      "name": "red",
      "excitation_nm": null,
      "emission_nm": null,
      "color": "#ff0000"
    },
    {
      "name": "green",
      "excitation_nm": null,
      "emission_nm": null,
      "color": "#00ff00"
    },
    {
      "name": "blue",
      "excitation_nm": null,
      "emission_nm": null,
      "color": "#0000ff"
    },
    {
      "name": "TRITC",
      "excitation_nm": 561,
      "emission_nm": 595,
      "color": "#ffbf00"
    }
  ],
  "dimensions": [
    "MULTICHANNEL",
    "Z_STACK"
  ]
}

[wasimxyz]

LGTM!