Review images in linked views¶
New in 0.16.0a4
Review Images requires 0.16.0a4 or newer. Use the manual version selector to match the software installed for your analysis.
Compare two aligned results with a familiar inspector sidebar: an intensity image beside its segmentation, red beside green, or an RGB composite beside a numeric colour-mapped result. Review Images changes presentation only. It does not calculate an image, run registration, or change measurements.
On the workflow canvas, Review Images is a compact node with Image A and Image B inputs and Open review…. It has no output thumbnail or No output placeholder: the images are reviewed in the separate window, not produced as a new node output.
Open a review¶
- Add Review Images and connect an image to Image A. Connect a second image, mask or labelled image to the optional Image B port.
- Calculate the upstream nodes. The review uses their current cached results; Open review… does not start an analysis calculation.
- Click Open review… on the node or in its inspector.
- Use the top toolbar to choose Side by side or Overlay and 2D slice or 3D volume. Above the left and right panes, select A, B, or A + B as available. For a volume, switching from 3D to 2D starts in the XY plane with Z navigation.
- Use the shared controls below the panes to select the T timepoint and
spatial slice, where those axes are available. Both panes always show the
same timepoint and slice. The editable number is the current position,
starting at 1; the total count appears separately as
/ N, followed by the calibrated coordinate. - Keep Link viewpoint enabled to rotate, pan and zoom together. Disable it to inspect the same timepoint from different viewpoints. Use Fit views beside the orientation buttons below the panes if the image is off screen. XY, XZ and YZ select orthogonal planes in 2D or aligned viewpoints in 3D. The slice control follows the remaining spatial axis (Z, Y or X). Oblique selects an angled 3D view when supported. These choices do not resample or transform the images.
Read-only · Native analysis resolution shares the bottom row with Oblique, XY, XZ, YZ and Fit views.
Use the top toolbar's Axes switch to show or hide the 3D orientation axes in both panes together. It is enabled by default and applies only to 3D views. The arrows and labels have a transparent background, not an opaque box over the images. This is display-only and does not change source pixels. Toolbar icons follow the active palette while retaining their text labels. Beside Axes, Scale bar shows or hides the scale bars in both panes, in 2D or 3D. It is enabled by default; a bar appears only where compatible spatial units support meaningful calibration. The bar's background is transparent.
Each framed pane joins its header/selector, native image view and footer title into one card. The review has its own napari panes and layers. It does not rearrange the main napari preview or carry a Crop outline into another workflow. Painting and label editing are disabled.
Both inputs must have explicit matching spatial/time grids, including axis names, spacing, units and origin. Equal dimensions alone are not enough. If they do not align, fix calibration or use Apply Transform upstream; Review Images never silently resamples or broadcasts one timepoint.
Choose the right presentation¶
| Inputs | Suggested left pane | Suggested right pane |
|---|---|---|
| Intensity and mask/labels | A | A + B |
| Red and green scalar channels | A | B |
| RGB composite and numeric index | A | B |
| Original and processed intensity | A | B |
For two scalar channels, choose their Colour map separately, for example Red and Green. Link A/B contrast is optional and off by default; enable it only when a shared numeric intensity scale is meaningful. The same input uses the same presentation wherever it appears in the two panes.
An RGB input keeps its original encoded colours; it does not offer a misleading scalar-colormap selector. Masks have a Foreground colour… and transparent background. Label IDs keep categorical colours rather than being stretched as scalar intensities.
Choose a scalar 3D presentation¶
In 3D volume, each scalar input has a 3D rendering choice:
- Maximum intensity (MIP) is the default: show the strongest value along each viewing ray.
- Depth-weighted intensity gives nearer structures more prominence. Adjust attenuation, initially 0.05, to change the depth weighting; it does not create opaque foreground occlusion.
- Surface (isosurface) shows a lit surface at a source-value display level. Set that level explicitly, or start at the midpoint of the black/white levels. A surface can hide interior structures.
Depth weighting and surface lighting change apparent brightness. For direct colour-scale/intensity inspection, use 2D slice or unshaded MIP instead; shaded views are not quantitative intensity review. In these shaded 3D modes, the bar is labelled Base colour scale (before shading). Lock colour scale protects black/white limits only, not shading or the surface level.
An A + B overlay of two scalar inputs is additive, not physically correct inter-layer occlusion. These choices do not affect RGB's labelled component-MIP adapter, Boolean mask surfaces or categorical label rendering.
Review a numeric colour scale¶
Set the scalar input's Black level and White level, enable Lock colour scale when that range has a fixed meaning, then use Hide below… and Visibility cutoff to suppress weak displayed values. The Fixed colour scale keeps the same mapping while the cutoff changes; the lock prevents accidental edits to its black/white limits. These controls do not threshold, clip or normalize the source array. Use an actual threshold node if you need a scientific mask.
Yellow in a red/green overlay is a visual cue, not a quantitative colocalization measurement. Review Images does not calculate RACC. A supplied RACC-like output remains numeric; its interpretation belongs to the RACC-like index reference.
Try the synthetic review examples¶
Open Open example… → Image Review and choose:
- Linked Red and Green Channel Review: change contrast independently, switch to Overlay and try linked viewpoints.
- 3D Intensity and Mask Review: rotate both panes together, change mask opacity, then switch to 2D slice. The authored mask contains two physical spheres with radii 5.4 and 5.0 µm on a 48×64×80 anisotropic grid; it has not been smoothed to improve appearance.
- Time-series Intensity and Label Review: move through four timepoints and verify both panes retain the same time and the original IDs 7 and 42.
- 3D RGB and Synthetic Index Review: review RGB slices beside a fixed 0–1 scalar colour scale. Change the visibility cutoff, not the colour scale.
The fourth example's index is a constructed spatial phantom, not a computed RACC or colocalization result. All four examples use synthetic data, not biological accuracy evidence.
Save and reopen¶
Review arrangement, pane choices, orientation preset, axes/scale-bar visibility, contrast, colormaps, opacity, visibility and per-input 3D rendering settings are saved in workflow presentation metadata. Save the workflow to retain them. Reopening a saved 2D review retains its selected XY, XZ or YZ plane; switching from 3D to 2D deliberately returns to XY. They are not scientific node parameters and do not invalidate upstream scientific results. Current camera position, timepoint and slice position are runtime navigation, not a new scientific transform or saved analysis parameter.
Keep a review open while editing¶
Edit and calculate upstream as usual; the review does not initiate recalculation. While reviewed inputs are changing or calculating, a visible review keeps the last complete pair clearly marked as waiting/noncurrent. Do not interpret that snapshot as the current result.
When both reviewed images have finished and their current results have been accepted, A and B update together automatically. On the same grid and with the same input kinds, the review preserves the view, contrast and display styles. Failed, cancelled, superseded or missing review inputs cannot become current.
Changes to the grid, image kind or connected-input presence require reopening the review when prompted. It never silently resamples the new data. Inputs for a visible open review are retained as presentation targets in Low-memory mode, but normal resource guards still apply; keeping a review open is not a way to bypass memory limits. Closing it does not close the main VIPP or napari window.
See Review Images reference for supported axes, rendering boundaries and qualification limits.