From 05927d81eef0a4e8c3fb9594c0bc43f936811628 Mon Sep 17 00:00:00 2001 From: Tristan Simas Date: Sat, 3 Oct 2026 04:36:23 -0400 Subject: [PATCH] Measure representative feature envelopes before scale selection --- .../raw-feature-envelope-guide-20261003.rst | 73 +++++++++++++++++++ .../references/measurement-interpretation.md | 22 ++++-- 2 files changed, 90 insertions(+), 5 deletions(-) create mode 100644 docs/validation/raw-feature-envelope-guide-20261003.rst diff --git a/docs/validation/raw-feature-envelope-guide-20261003.rst b/docs/validation/raw-feature-envelope-guide-20261003.rst new file mode 100644 index 0000000000..5323644e75 --- /dev/null +++ b/docs/validation/raw-feature-envelope-guide-20261003.rst @@ -0,0 +1,73 @@ +Representative feature-envelope guide: source-only continuation +============================================================== + +Canonical owner and scope +------------------------- + +The original knowledge manifest maps ``openhcs_measurement_interpretation`` to +``packaging/codex/openhcs/skills/use-openhcs/references/measurement-interpretation.md``. +The original plugin skill bundle packages that same source; no new manifest, +generated guide, copied parameter catalogue or runtime policy is introduced. +Canonical reStructuredText entry/reference documents remain unchanged. + +Existing guidance already requires distributed raw measurements, earliest-stage +diagnosis, one semantic change, regression controls and bounded development. +Its smoothing/spot/ridge evidence row nevertheless named only the narrowest +supported width. The edit replaces that incomplete sampling description with +an observed width/size/intensity envelope and explicit positive/faint controls. +It requires reflection of a compatible callable before a multiscale comparison, +including actual units/arguments/combination semantics and response-memory cost. +It promises no available filter, parameter name, scale setting or biological gain. +Claim-level conclusions link to the existing strategy owner rather than copy it. + +Complete use-openhcs and Diataxis skills plus the relevant measurement and +installation references were read. Diataxis keeps this a working how-to +correction inside the current procedure. No scientific context, report, images, +pipeline settings, reference answers or object identities were consulted. + +Ownership and preserved source +------------------------------ + +Current remote main is f7de9efad393bce83a3756a271f0cd4383783ea9. Existing isolated +``openhcs-input-preparation-20260929`` was reused non-recursively on a docs branch; +no new worktree, environment or package was created. Planck confirmed no borrower +of this checkout. Foreign dirty submodules remain untouched and excluded. +Published catalog511/b1d0b6c3e and its immutable qualified target are preserved. + +Singer owns the separate viewer-retirement guide seam. Current guide520 already +distinguishes hiding from buffer release and preserves saved/current evidence, +but does not name the actual producer-incarnation request or measured memory +comparison. The target's real request takes ``expected_producers`` from complete +``producer_identities`` (including invocation key), not guessed route names. +Singer was asked to publish that correction through a new source-only guide PR; +this change does not edit his guide or runtime family. + +Actual target04 check, not a new qualification +-------------------------------------------- + +Readonly target: ``engineering494/target04`` under the existing batch root. +Authoritative originals: ``READY-MAIN13.json``, ``PACKAGE09-QUALIFICATION.json`` +and ``package08.log``. The ordinary wheel's SHA256 is +``d3cb03f47c2831a6287a6f510de931efcc861bd7c8c43a8076704eae074b3639``. +Original build source b26334ace99512970c81809b29d5ad19c7e07c4c; reviewed source +24927b864e3c7bc7e413f9929fbf917a5973ea5e. Planck confirms original full source, +knowledge and13-skill equality; no whole-wheel verification was rerun here. + +Direct comparisons show installed strategy/custom-authoring/viewer-QA bytes equal +released511 b1d. Installed hashes: + +* strategy: d9fef83e84a1d1cea928c9207971f8516ced350b5219b5c7f770dcb458e2710a; +* custom: 794b3ebab69e0256eeffeec4a2f683e9d82cc682e78aae43f6bcbe57da05b43d; +* viewer: 416e65e2e1745bd2547506ee97970d123cd8595a55dfc37be4fb00693daa2d90; +* measurement: fb25ac9aa3b777f775daa76242546406642d2a75b587ae8adb81ca74f18cfdd0. + +Installed capability/DTO source exposes ``openhcs_retire_viewer_window_layers`` +and its typed producer proof; the original guide bytes remain generic520 wording. +The522 validation/receiving notes are published source, not manifest-projected +knowledge resources. No claim is made that they were added to the installed skill. + +This new measurement correction is NOT in target04. It needs normal source review +and future package qualification; no hot sync, import, test, build, install, +client/native/UI/provider call or scientific contact occurred. Frozen evaluations +and previous failure dispositions remain immutable. Source diff/link review is +not public installed retrieval or biological acceptance. diff --git a/packaging/codex/openhcs/skills/use-openhcs/references/measurement-interpretation.md b/packaging/codex/openhcs/skills/use-openhcs/references/measurement-interpretation.md index cf410a9f68..7908944230 100644 --- a/packaging/codex/openhcs/skills/use-openhcs/references/measurement-interpretation.md +++ b/packaging/codex/openhcs/skills/use-openhcs/references/measurement-interpretation.md @@ -16,10 +16,13 @@ measurements, not ground truth or an automatically validated parameter choice. canvas pixels are not source pixels. World coordinates must be converted through the layer transform before becoming index-space sample coordinates. 2. Choose clear isolated objects, a genuine close pair and faint/small examples - across preselected bright/dim, sparse/dense and centre/edge regions. Retain - extremes and ambiguity rather than measuring only objects the current - detector finds. For 3-D, inspect multiple Z planes and orthogonal views when - exposed; a projected width does not establish Z extent. + across preselected bright/dim, sparse/dense and centre/edge regions, at context + and native feature scales. Measure an envelope of supported widths, sizes + and local signal/background values, including narrow and broad structures, + clear positives and faint controls. One early feature is not the assay's + scale range. Retain extremes and ambiguity rather than measuring only objects + the current detector finds. For 3-D, inspect multiple Z planes and orthogonal + views when exposed; a projected width does not establish Z extent. 3. Use exposed native measurement capabilities where available and retain their receipts. For bounded raw evidence, `openhcs_sample_viewer_window_image` takes `route_key`, route-local `axis_indices`, native `y`, `x`, `height`, @@ -40,7 +43,7 @@ measurements, not ground truth or an automatically validated parameter choice. | --- | --- | --- | | Object-size range | Long/short raw boundary spans across isolated and touching examples; per-axis extent for 3-D | Calling a current mask's size independent evidence, or confusing radius with diameter | | Seed separation | Centre-to-centre distance of genuine neighbours and multiple maxima within one textured object | Using diameter as minimum separation and suppressing real close pairs | - | Smoothing/spot/ridge scale | Narrowest supported feature width, noise texture and nearby close-pair/path control | Equating diameter with Gaussian sigma or erasing a faint neurite | + | Smoothing/spot/ridge scale | Supported narrow-to-broad width envelope, noise texture, positive/faint-path and close-pair controls | Equating diameter with Gaussian sigma or assuming one scale preserves every supported width | | Background-removal scale | Target width plus extent and variation of nearby background in multiple regions | A universal kernel radius or subtracting cell signal as background | | Threshold/prominence | Raw object-versus-local-background values, weak positives, noise and saturation on the consumed channel | Deriving analytical thresholds from contrast limits, gamma or label colours | | Roundness/shape prior | Isolated raw contours, elongated/lobed examples and an unsupported-shape control | Forcing every cell to be round or treating a round-looking mask as validation | @@ -61,12 +64,21 @@ measurements, not ground truth or an automatically validated parameter choice. differ between algorithms. Keep unsupported precision as an interval or limitation. Label mask-derived estimates provisional and check against raw, including missed objects; do not tune a detector solely from its own output. + A single-scale filter can favour one width class while suppressing another. + Inspect its response across the measured envelope before changing downstream + thresholds. If discovery returns a compatible multiscale callable, describe + its actual scale units, supported arguments and response-combination contract; + do not invent a scale-list parameter or assume a single-scale argument accepts + one. Estimate intermediate/response memory before a bounded comparison. 6. Compile one bounded candidate, inspect its earliest changed intermediate, then compare matched raw/result/combined at the measured failures and regression controls. Revisit distributed regions after every change; a local repair can fail elsewhere under uneven illumination. Freeze measurement receipts and rationale with the complete candidate before held-out access. Expected counts or reference masks must not choose measurements in a blind run. + Link the measured envelope and remaining exclusions to the affected phenotype + claims through [the analysis strategy](analysis-strategy.md), which owns + claim-scoped conclusions rather than blanket abstention. ### Native ruler, profile and independently specified region operations