Example Workflows

The release contains 13 example workflows under:

examples/

They are intended for regression tests, screenshots, tutorials, and manual review.

In VIPP, open them with:

Open example...

The chooser groups workflows by task and opens each template with its bundled sample Image Source nodes already configured. Use Load workflow... for custom or external workflow JSON files.

Workflow Index

Workflow	Input sample	Purpose
synthetic-batch-provenance.json	generated two-source NumPy collection	Three paired items, explicit NPY/TIFF/TSV outputs, representative navigation, saved config/runner, exact ground truth, manifests, archives, and item sidecars. Open it through the chooser and create a writable working copy.
otsu-red-channel-labels.json	synthetic multichannel volume	Label cleanup: split the red/TRITC-like channel, blur, Otsu threshold, mask cleanup, connected components, border clearing, and volume filtering.
red-channel-object-intensity-measurements.json	synthetic multichannel volume	Multi-input object measurement using labels plus matching intensity image.
red-channel-merged-measurement-table.json	synthetic multichannel volume	Morphology, intensity, table merge, and metadata columns.
synthetic-measurement-summary.json	synthetic measurement summary	Grouped object-count and area summaries.
synthetic-derived-object-morphology.json	synthetic object morphology	Derived 2D morphology, circularity, perimeter/area ratio, Hu moments, and column selection.
synthetic-3d-mesh-morphology.json	synthetic 3D mesh morphology	Surface area, mesh volume, convex hull, sphericity, and tiny-object status.
synthetic-skeleton-qc.json	synthetic skeleton network	Skeleton keypoints, component/branch labels, pruning, branch tables, graph tables, and network summaries.
synthetic-advanced-skeleton-network.json	synthetic advanced skeleton network	Time-indexed 3D skeleton graph stress test.
synthetic-colocalization-racc.json	synthetic colocalization	Pixel and ROI-masked colocalization, scatter thresholds, colocalized voxels, and RACC-like output.
synthetic-object-colocalization-association.json	synthetic colocalization	Object colocalization, label overlap, nearest distance, event localization, and merged tables.
synthetic-deconvolution-rl-tv.json	2D deconvolution image plus measured PSF	2D measured-PSF restoration with ordinary RL and RL-TV.
synthetic-3d-deconvolution-rl-tv.json	3D deconvolution volume plus 3D measured PSF	Volumetric PSF-aware restoration.

Launcher Names

Use:

python scripts\launch_vipp_intensity_workflow.py <name>

Use --list to print the release's exact IDs. In 0.12.0a3 they are:

ID	Example title
batch-provenance	Deterministic Batch & Provenance
label-cleanup	Red-Channel Label Cleanup
object-intensity	Object Intensity Measurements
merged-measurements	Merged Measurement Table
summary-table	Grouped Measurement Summary
derived-morphology	Derived 2D Object Morphology
mesh-morphology	3D Mesh Morphology
skeleton-qc	Skeleton QC
advanced-skeleton	Advanced Skeleton Network
racc-colocalization	RACC Colocalization
object-colocalization	Object Colocalization Association
deconvolution-2d	2D Richardson-Lucy / TV Deconvolution
deconvolution-3d	3D Richardson-Lucy / TV Deconvolution

Legacy launcher aliases such as intensity, merged, and mesh remain for maintainers, but documentation should use the canonical IDs above. An unknown ID is an error; it does not silently open another example.

Adding A Core Example Workflow

When adding a new core example:

1. Add a deterministic bundled sample or document the input source.
2. Save workflow JSON under examples/.
3. Add a row to this page and the repository example README.
4. Add a launcher shortcut if it is used often.
5. Add a focused test that checks the expected output type and one meaningful invariant.