Validation status¶
This page summarizes the evidence shipped with the 0.12.0a3 application source. It is a claim boundary, not a certificate that every node is validated for every assay.
Evidence available now¶
- automated tests cover graph behavior, persistence, previews, export, operations, UI behavior, I/O routes, and bundled examples;
- architecture tests enforce the Qt-free
core/dependency boundary, and focused tests cover stable source revisions, physical grids, detached snapshots, atomic persistence, typed execution, and stale-result rejection; - 13 deterministic synthetic samples and 13 checked-in workflows support regression checks and inspection;
- a generated two-source batch bundle exercises three paired items, nine exact NPY/TIFF/TSV outputs, workflow/config hashes, source identities, manifests, archives, and three finalized item sidecars;
- an analytical phantom report exercises calibrated object/mesh morphology;
- method notes and focused tests cover colocalization calculations;
- tables, CSV/TSV writing, workflow JSON, and Python generation have automated behavior checks; and
- focused UI/execution tests cover isolated-tuning boundaries, actionable and waiting stale states, progressive node previews, compatible layer reuse, and rejection of stale contrast/histogram results; and
- batch tests cover attached-config validation and round-trip, restore without preview, direct plan-only execution, complete-item fast skips, transient atomic-write retries, and continuing after a final item-sidecar failure.
Release CI covers package/manifest, lint, and test behavior on Linux and Windows. A passing CI matrix is not equivalent to a manual GUI smoke pass on every operating system, Qt/display environment, filesystem, or microscope reader.
A bounded manual Windows acceptance pass for 0.12.0a3 covered direct
unpreviewed batch execution, complete Skip items, continued processing after
an item failure, attached-config save/reload, and a representative 3D
deconvolution batch. It does not establish cross-platform behavior, broad
filesystem interoperability, large-collection scalability, or restoration
quality for arbitrary samples.
The release's generated calibrated-morphology report records 28/28 checks passed. Its own scope excludes broad numerical equivalence, biological interpretation, and all data conditions. The application test suite checks that the report remains synchronized with the validation script.
Do not generalize this evidence into¶
- usability superiority over other tools;
- broad equivalence to Fiji, CellProfiler, scikit-image, or another package;
- scalability to whole-slide or high-content datasets;
- complete OME/acquisition metadata fidelity;
- biological validity of a segmentation, restoration, or measurement workflow;
- user-study evidence beyond explicitly described pilot observations.
High-priority evidence gaps¶
Passing deterministic tests is valuable internal evidence, but it is not the same as an external comparison or assay validation. The distinction matters:
| Area | Current in-repository evidence | Next evidence needed |
|---|---|---|
| Watershed/object separation | Touching-disk split tests, exported-workflow execution, and 3D-default behavior tests | Broader 3D phantoms, split/merge metrics, external comparison, representative real images |
| Colocalization/association | Deterministic metric, overlap, distance, and association tests plus synthetic examples | External numerical comparisons and assay-specific positive/negative controls |
| Skeleton networks | Synthetic network workflows and focused operation tests | Prespecified topology and calibrated-length packs, perturbation tests, external comparison |
| I/O and metadata | Focused format, dtype, validation, and round-trip tests | A release-pinned field matrix and licensed corpus of representative microscope files |
| PSF/deconvolution | Deterministic 2D/3D synthetic images, measured-PSF samples, and operation tests | Real bead PSFs, representative microscopy images, artifact/noise analysis, performance characterization |
| Sources and physical grids | Revision-change, owned-snapshot, stale-worker, semantic-axis, scale/unit/origin, mask-broadcast, and image/PSF grid tests | Independent corpus covering live readers, network filesystems, registration histories, and heterogeneous microscope metadata |
| Large data/batch | Functional cache/path/memory tests plus deterministic attached/standalone config, planner, direct plan-only execution, source verification, complete-item fast skips, staging, retry, manifest/archive, sidecar, collision, replay, continuation, exact-output bundle, and a bounded Windows acceptance pass | Representative memory/time benchmarks, forced-process interruption studies, large collection stress tests, cross-platform/cloud-filesystem studies, semantic-axis iteration, and HCS traversal |
| Workflow/export architecture | Schema-3 rejection/round-trip, optional batch-attachment validation, snapshot materialization, atomic-write failure, shared-executor export, multi-source binding, and runtime-version tests | Independent reproducibility exercises across archived environments and long-lived release migrations |
| Usability | No release-pinned public usability study | Ethics-reviewed, preregistered task study with a controlled comparator and neutral outcomes |
Release-specific limitations¶
- Workflow schema 1 and 2 are intentionally rejected; 0.12.0a3 has no automatic migration.
- Valid 0.12.0a1 and 0.12.0a2 schema-3 workflows load structurally, but cached pixels/tables are not serialized and exported Python is runtime-version pinned. Recalculate, regenerate exports, and validate after upgrading.
- Batch processing is local-file and sorted-position oriented. It does not iterate selected T/C/Z combinations or discover plate/well/field structure.
- Many operations are eager even when a source format supports lazy/chunked access; background execution improves responsiveness, not total work.
- Declared-grid validation cannot prove biological registration or metadata truth. It can only enforce the axes/calibration supplied to VIPP.
- Richardson-Lucy/TV controls and synthetic tests do not establish a validated restoration parameter range for a real microscope or assay.
- Manifest and item sidecar writes improve recovery evidence but are not one transaction across all outputs and provenance files.
For your workflow¶
Use validate a workflow to choose assay-specific evidence. If a public claim depends on a gap above, label it as a limitation or produce the required evidence before making the claim.