feat(converter): automatic channel color detection#47
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Add bioio_conversion.channel_colors with get_channel_colors(), which derives an OME-Zarr display color per channel, and wire it into OmeZarrConverter so channels are colored automatically instead of all defaulting to white. Color policy (per channel): - Brightfield / transmitted-light channels -> white, and do not consume a fluorescent palette slot. Detected via OME contrast_method / illumination_type with a channel-name fallback. - Recognized fluorophores -> their true emission color via the FLUOROPHORE_COLORS table (e.g. GFP -> green, AF647 -> red). - Remaining channels -> a count-based, perceptually-distinct palette (green / green+magenta / cyan-yellow-magenta / +Okabe-Ito), ordered by emission wavelength when available. Black is never assigned. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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| """Lower-case ``text`` and strip every non-alphanumeric character. | ||
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| This collapses fluorophore spellings to a canonical token so that, e.g., | ||
| ``"Alexa Fluor 488"`` and ``"AF-488"`` both reduce to a comparable form. |
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This comment confused me; the outputs of the two examples would "af488"
"alexafluor488" don't compare to each other, but rather match a value in the COLORS dict.
Maybe the example should be
"Alexa Fluor 488" and "ALEXA FLUOR-488" collapse to "alexafluor488" to allow a match with value in FLUOROPHORE_COLORS
kmitcham
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Jul 7, 2026
…colors # Conflicts: # bioio_conversion/__init__.py # bioio_conversion/converters/ome_zarr_converter.py
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Summary
Resolves #25
Adds automatic channel display color detection to the OME-Zarr converter. Previously every channel was written with a hardcoded white (
#FFFFFF) OMERO color; now each channel gets a meaningful color derived from its metadata.This ports the recipe from #42 (the standalone
get_channel_colorsexperiment) and wires it intoOmeZarrConverterso colors are assigned during conversion without any caller changes.Color policy (applied per channel)
contrast_method/illumination_type, with a channel-name fallback (BF,TL,DIC, "phase contrast", …).FLUOROPHORE_COLORStable (e.g. GFP → green, TaRFP → orange, AF647 → red). Matches the OMEfluorfield or the channel name.So identity wins when known, and the distinct palette fills the rest.
Changes
bioio_conversion/channel_colors.py—get_channel_colors()plus the fluorophore/brightfield/palette helpers. Exported from the package__init__.OmeZarrConverter._resolve_channels— derives per-channel colors viaget_channel_colorsinstead of hardcoding white. Explicit user-suppliedchannels=still take precedence; no-channel-axis behavior unchanged.bioio_conversion/tests/test_channel_colors.py— 24 tests.Verification
s_3_t_1_c_3_z_5.czi: EGFP→green, TaRFP→orange (FFA500), Bright→white — confirmed in the written OMERO metadata.🤖 Generated with Claude Code