Inspect and compare outputs

VIPP has several inspection surfaces. Choose the one that answers the question rather than treating a thumbnail as evidence for every decision.

Surface	Good for	Not sufficient for
Node thumbnail	Rapid whole-graph scan	Fine boundaries, rare failures, or quantitative QC
Inspector preview	Selected node at a controlled slice/MIP	Comparing many full-resolution layers
Pinned napari layer	Full-resolution comparison and overlay	Recording why a parameter was selected
Histogram	Dynamic range and threshold context	Spatial correctness
Label-volume histogram	Size-filter cutoff review	Shape or identity correctness
Table preview	Columns, rows, units, obvious missingness	Statistical validation of measurements

Read Display Summaries Correctly

An inspector histogram counts every finite value in the chosen slice or stack, then groups those counts into a compact chart. Its chart bins are independent of the saved Float histogram bins used by histogram-based automatic threshold nodes. Changing plot log scale or appearance does not change the mask.

The colocalization scatter density, ROI population, and colocalized count are also calculated over every ROI voxel. On a large input, wait for the exact background calculation to finish before capturing a QC screenshot.

Napari contrast limits are display-only. For a large inspect or pinned layer, VIPP may show an explicit provisional dtype range first and replace it with the exact full finite range when the background calculation completes. A manual contrast adjustment made while waiting is preserved. Neither range changes the node output or downstream measurements.

Pin an output in napari

1. Select a node with an image-like output.
2. If it has several outputs, select the intended output port.
3. Choose Pin selected.
4. Rename the napari layer if necessary so the operation and parameters remain recognizable.

Pin the raw image, a decisive intermediate mask, and the final labels for an overlay review. Hide or show layers to locate false positives, missed objects, merged objects, and boundary errors.

Compare 3D data without hiding failures

A maximum-intensity projection can make a workflow look persuasive while hiding slice-specific noise or z-merging. Review at least:

• representative YX slices at multiple z positions;
• the volume/MIP overview;
• objects near the top and bottom of the stack;
• regions with low signal or high background;
• anisotropic structures when z-spacing differs from x/y pixel size.

Use Link napari/VIPP sliders when synchronized slice navigation is useful. Turn it off when the inspector should remain on a fixed reference slice.

Review manual results after upstream changes

Manual/cached nodes become stale after a relevant upstream or parameter change. Select the node and choose Recalculate, or use Calculate all for all stale manual nodes. Do not take a screenshot or export a table while its status indicates a stale cached result.

Capture review evidence

For a formal analysis, retain representative QC images or screenshots with:

• input/sample identity;
• workflow and VIPP version;
• slice or projection mode;
• visible scale and units where relevant;
• enough context to identify the operation and parameter being reviewed.

Screenshots complement reference masks and quantitative tests; they are not a replacement for them.