Inspection Model

The point of VIPP is not only to run a pipeline. It is to make each processing decision inspectable.

Inspection Surfaces

Surface	Use
Node thumbnail	Quick scan of what each stage is doing.
Napari inspect layer	Full-resolution inspection of the selected node output.
Pinned layer	Keep important outputs visible while editing other nodes.
Histogram panel	Check intensity distributions and threshold choices.
Input histogram	Review cutoffs for threshold-like nodes.
Label-volume histogram	Tune label filtering against the incoming object-size distribution.
Table preview	Check measurement columns, row count, and units before export.
Graph notes	Record why a parameter or branch exists.

Calculation And Display Are Different Contracts

VIPP separates a node's declared scientific calculation from the compact view used to draw it. Where a complete-population summary is described below, every required value contributes even though the result is grouped for display.

Inspector item	What is exact	What is display-only
Intensity histogram	Every finite value in the selected slice or stack is counted.	Counts are grouped for drawing: two bars for Boolean data, one for a constant image, 256 for non-negative integer data within 0–255, and otherwise 128 display bins. These bins are not the automatic-threshold bin setting.
Automatic-threshold guide	The guide uses the node's saved scope and scientific method parameters.	Line colour, plot scale, and the chart's display bins do not change the mask.
Colocalization scatter	Every ROI voxel contributes to the 255 × 255 density grid; ROI population and the number meeting both thresholds are also exact.	Colormap, logarithmic count display, and guide styling do not change thresholds or results.
Inspect or pinned image contrast	The final display range spans every finite value and zero, using exact finite extrema.	Contrast limits affect only rendering in napari, never the stored node output or downstream calculations.

Progressive inspection during a run

As each node completes in a background run, its card becomes current and its sampled thumbnail updates immediately; later cards can still be calculating or waiting. If the active cache policy already retains that node, selecting or pinning it and opening its table or metadata uses the same newly completed run-scoped payload. An otherwise prunable Low-memory intermediate gets the card state and thumbnail without forcing VIPP to retain its full-volume payload.

This is a progress view, not a partial scientific commit. VIPP publishes the new workflow cache only when the complete run is accepted against the same graph and source revisions. Cancellation, failure, a newer edit, or a superseding run removes the temporary overlays and restores the last coherent inspection state.

Reused and replaced napari layers

Compatible generated Image results reuse the same napari layer object. VIPP replaces its data reference with a non-writeable view of the exact output and resets colormap, blending, contrast, scale, and related metadata. This avoids a duplicate full-volume copy and prevents display choices from the previously selected node leaking into the new one. Any pending contrast result for the old selection is invalidated.

VIPP creates a replacement layer when the presentation class or layout is genuinely incompatible, such as Image versus label-ID Labels, or an RGB layout change. A Boolean mask pinned as a Labels overlay requires a uint8 presentation copy. The original cached Boolean array remains the scientific output used by downstream nodes and saving.

Large generated layers

When an inspect, pinned, or RGB-channel layer is large, VIPP first supplies a provisional dtype-based contrast range so napari can show the layer without scanning it on the user-interface thread. VIPP then calculates the exact full finite range in the background and updates the layer.

This temporary range does not mean the processing result is approximate. It is only a display window. If you manually adjust the napari contrast limits while the exact calculation is pending, VIPP keeps your adjustment rather than overwriting it; the exact finite range remains available in the layer metadata.

For large inputs, exact histogram guides, colocalization summaries, Auto Contrast, and generated-layer ranges may briefly show a calculating state. Selecting another node or changing the input invalidates stale display results.

Dragging a manual input-histogram guide does not change the input population. VIPP therefore retains the exact displayed counts while moving Binary Threshold, Hysteresis, or explicit Rescale/Clip guides, and recalculates only the node output after the short interaction delay. Its output histogram then refreshes because that population really did change. Parameters that change an automatic guide refresh that guide separately. A different connected image, slice, or histogram scope still invalidates the input counts because it selects a different population.

For Rescale Intensity, both low and high input guides are draggable. Dragging a guide derived from exact percentiles changes the cutoff mode to explicit values, retains the other exact cutoff, and recalculates the node. A click that does not move the guide is not an edit. The same no-movement rule prevents accidental Binary Threshold changes. Save the workflow after accepting a drag; guide position is a presentation affordance for a persisted scientific value.

Split Channels presentation output

Split Channels produces one scientific graph output per channel, but its node card and inspector need one channel to present at a time. If downstream connections use exactly one distinct output port, VIPP presents that channel in the split node's thumbnail, napari inspect or pinned layer, histogram, output metadata, dimension controls, and Save selected output... action. Multiple branches may consume the same port; that remains one distinct used output.

If no output is connected, or the graph uses two or more different channel ports, these presentation surfaces use the saved Thumbnail channel instead. The automatic choice never changes Thumbnail channel, rewires a connection, or alters the arrays supplied to downstream calculations. It only keeps all ways of inspecting the Split Channels node focused on the same unambiguous channel.

Recommended Inspection Sequence

For segmentation:

1. Inspect the raw channel.
2. Inspect background correction or denoising.
3. Inspect the threshold mask.
4. Inspect label IDs.
5. Inspect measurement tables.
6. Save the workflow only after the intermediate stages make sense.

For colocalization:

1. Inspect both channels separately.
2. Inspect the ROI mask if used.
3. Inspect scatter/threshold guides.
4. Inspect colocalized voxels.
5. Inspect metric tables.

For skeletons:

1. Inspect the binary mask.
2. Inspect the skeleton.
3. Inspect keypoints or graph overlay.
4. Inspect branch/component labels.
5. Inspect measurement tables.