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Add composite intracellular species coloring - #32

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marpaia merged 5 commits into
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marpaia/19
Sep 25, 2026
Merged

marpaia merged 5 commits into
masterfrom
marpaia/19

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@marpaia marpaia commented Sep 24, 2026 •

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Add a Species composite view for co-expression: select channels, set individual tints and shared per-channel scalar ranges, and combine normalized contributions in linear RGB. Full red/green expression yields yellow; disabled channels contribute nothing, and disabling all channels shows neutral gray with an explicit legend. Existing species and categorical views remain available.

Channel names, tints, bounds and order appear in the controls and legend. Preferences remain keyed to numerical channels through missing data, reset and seeking. Single/composite editors share each species range and synchronize active values while preserving pending edits during ordinary frames.

Validation: 66 viewer tests; TypeScript/build/format checks; actual Chromium instance-color assertions and inspected screenshots covering red/green/co-expression/zero, half-intensity color-space math, saturation, toggling/reordering, shared ranges, invalid tints, moving frames, picking/highlighting/lineage and dataset transitions. The actual replay timeline passed combined campaign verification.

Originally reviewed against frozen marpaia/base-19, combining #15/#20 and #18. Prerequisites were integrated before retargeting to master. No native kernels changed.

Closes #19.

Independent review is complete against the original acceptance criteria and intended review base. The review report records per-criterion evidence, both corrected campaign findings, exact tested heads, landing order and platform limits.

Merged into master in the approved campaign order: #26, #27, #28, #31, #34, #36, #29, #30, #33, #35, #37, #32. The final tree preserves the reviewed implementation and integration regressions. Prerequisites were integrated with merge commits, and the frozen review bases were retained.

Landing validation: 534 Python tests passed (57 environment-dependent skips), 115 viewer tests passed, Ruff lint, strict type checks, viewer build/format checks, and actual Chromium feature/integration checks passed. Pyright retains the existing native-extension source warning. A Windows-only documentation link-test encoding failure was reproduced and fixed with an explicit UTF-8 read; the corrected final PR heads passed Windows CLI/shutdown checks and CUDA compilation. NVIDIA runtime execution remains unverified.

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Add simultaneous coloring by multiple intracellular species

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