Document the before/during/after segmentation workflow with one shared MorphoBricks step pattern #167

Problem

The notebook now exposes the repository well, but it does not clearly communicate an important capability of the core:

• preprocessing can run before segmentation with no masks;
• it can run during segmentation with partial masks (mask_missing is a warning);
• adding masks later does not recompute image histograms;
• preprocessing should be refreshed after masks are added before downstream bricks consume the run;
• interrupted image preprocessing resumes from staged completed FOVs.

The full user guide contains most of these details, but the notebook should give a minimal reusable explanation rather than another long manual.

Suggested notebook pattern

Use the same short explanation pattern in MorphoBricks notebooks:

What this step does: Processes the selected inputs and records the result for later MorphoBricks steps.
What is checked: Inputs and recorded metadata are validated first; missing scientific information is never guessed.
Safe to rerun: Unchanged completed work is reused. If interrupted, run the step again to continue from valid completed work.
Incomplete inputs are OK: Available results are processed now; missing results remain pending and can be added later. (Only where true.)

For preprocessing, the page-level wording should make clear:

• Check inputs: current masks are optional and missing masks are reported.
• Confirm image interpretation: axes/image type are explicit; nothing is guessed.
• Process: histograms are resumable/reusable; adding masks later does not recompute them.
• Review: QC/statistics are optional and do not change downstream preprocessing data.

Keep the notebook concise; detailed edge cases stay in the user guide/status cards.

Release-smoke coverage

Extend the Colab + JupyterLab/LabConstrictor smoke check with one lifecycle scenario:

1. preprocess images with no masks;
2. add a partial mask set and rerun: histogram images are not reread, missing masks are reported;
3. add more masks and rerun: unchanged histogram work is still reused;
4. interrupt a mask scan and resume it once per-FOV mask-scan staging exists;
5. finish segmentation and verify the final incremental mask report matches a clean full scan;
6. add/change a mask after the final run and verify downstream RunInputs refuses the stale run until preprocessing is refreshed.

Acceptance

• Notebook intro/page text stays short and readable.
• The segmentation lifecycle above is explicit.
• The same wording pattern is suitable for reuse across other MorphoBricks notebooks.
• The release checklist tests the lifecycle in both supported notebook environments where applicable.