Validate a workflow¶
Validation asks whether a frozen workflow produces sufficiently accurate and stable outputs for a defined use. Passing software tests shows that code behaves as specified; it does not establish biological validity for your data.
Match evidence to the claim¶
| Claim | Useful evidence |
|---|---|
| An operation matches its mathematical definition | Unit tests, analytical phantoms, numerical comparison to a documented reference |
| A file route preserves required information | Round-trip fixtures, metadata assertions, visual inspection of representative real files |
| A segmentation identifies the target | Blinded reference annotations, object/boundary metrics, error taxonomy across representative conditions |
| A measurement is quantitatively accurate | Calibrated phantoms or objects with known dimensions/intensities |
| A workflow is robust | Held-out data across acquisition days, operators, biological conditions, and known artifacts |
| Users can complete a task | Preregistered usability protocol and task evidence—not developer observation alone |
Build a reference set¶
Define the unit of analysis and sampling frame. Include ordinary cases and predefined hard cases. Reference annotations should have documented rules; for subjective targets, measure agreement between annotators and resolve ambiguous cases without using the workflow output as the authority.
Report more than one score¶
For segmentation consider object detection, splits/merges, pixel overlap, boundary error, and count/size bias. For measurements examine error across the range, not only correlation. For spatial association use deterministic geometries with known overlap/distance before interpreting biological samples.
Always show representative failure cases and uncertainty. Select examples by a predefined rule or show a balanced range, not only the most attractive field.
Keep validation independent¶
Do not use the held-out set to choose parameters. Freeze the workflow and software environment first. Record any failed items, exclusions, retries, or manual interventions.
Read VIPP's own evidence conservatively¶
The validation status lists evidence in the application repository and important gaps. Those checks support software-level claims; they do not validate a specific biological workflow for you.