GrayToColor STACK native control rejects runtime channel-plane metadata #432

Observed live failure

The registered GrayToColor STACK route fails in native execution before retaining a raw image reference. It currently prevents an analysis pipeline from retaining raw Calcein body input, separately capping outgrowth input, and composing the two processing-role images without modifying acquisition identity.

Installed OpenHCS source is merged PR430 fa04956a7eb3212e3456cf9927fc35ab6cdfd361, PolyStore public 0.3.1. Fresh native server and current function catalog are ready. No timeout/restart is involved.

Two independently submitted compiled control documents fail at their first RetainRawCalceinBodyReference step:

GrayToColor image metadata requires a source-binding plane axis,
got <RuntimePlaneAxis.RUNTIME_SLICE: 'runtime_slice'>.

Original execution IDs: 37f69b64-2331-4bcb-a4f1-99f78da3d316 (v1), c81af5db-f805-434a-a067-930d5201975c (v2 explicit input selector). Both are terminal failures on the same original native process; failed calls are retained, not replayed.

Public declaration recipe

Use a normal SourceBindings acquisition with scalar 2D files: w1=DAPI/C1, w2=FITC-Calcein/C2. Select only FITC at the first step. Each relevant step groups by NONE and declares variable component CHANNEL. The complete control contains:

1. Registered gray_to_color, scheme STACK, rescale_intensity=False, name output raw_calcein_body_reference, pipeline-start FITC ingress.
2. Registered skimage:exposure.rescale_intensity, in_range=(0,6000), out_range=(0,1), previous-step input.
3. Registered gray_to_color STACK, no rescale, name output capped_calcein_outgrowth.
4. Registered gray_to_color STACK, no rescale, repeated image_name=(raw_calcein_body_reference,capped_calcein_outgrowth).

v2 explicitly supplies the first step's FITC input selector but reaches the same metadata failure. The control fails before its later numeric/role-preservation checks; it is not an accepted scientific pipeline. A third attempt to declare a stack axis on a physically scalar 2D source fails compilation and is a separate authoring error, not evidence that the runtime should accept fabricated axes.

Original evidence and ownership

Persistent original control sources and script stdin/stdout/timing are at /home/ts/wt/openhcs-issue-batch-20260929/neurite-development-skill383-20261001/output/assisted-3-fa049/. v1/v2 failures occur at original mcp.stdout lines 5365–5421 and 6724–6780. Native PID3214331/port5993 remains owned by the scientific author; do not replay its failed submissions or mutate the live environment.

Schrodinger owns source diagnosis/minimal synthetic reproducer and the independent color declaration/backend surface. Root in PR394 retains generic executor/input-context, source metadata/projection and shared materialization ownership. Dalton owns scientific authoring and checks other existing declaration-compatible routes. No competing generic implementation is authorized.

The source diagnosis must establish whether an admissible channel/named-image ingress receives incorrect plane metadata, or whether a different current public authoring contract is required. Do not remove the guard before proving that relation.

Acceptance

Prove the correct public declared route with a synthetic source-bound control through the real compiler/executor, preserving raw plane values, exact physical source/channel identity, order, axes, spacing and capped-plane units. Wrong/undeclared spatial axes must still fail. Reuse the existing declaration, nominal projection/binding and carrier owners; no manual relabeling, filename identity, blanket squeezing or permissive catch-all axis handling.

Publish the reproducer and tested repair/proposal in a linked draft PR. After source review and actual installation at a safe stopped checkpoint, exercise the original installed MCP/native control before claiming readiness. Current runs remain assisted development; held-out data is sealed.